8USB

Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1

PDB DOI: https://doi.org/10.2210/pdb8USB/pdb
EM Map EMD-42506: EMDB EMDataResource

Classification: HYDROLASE/PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3), Homo sapiens
Mutation(s): No

Deposited: 2023-10-27 Released: 2024-11-06
Deposition Author(s): Arkinson, C., Gee, C.L., Martin, A.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome

Arkinson, C., Dong, K.C., Gee, C.L., Costello, S.M., Marqusee, S., Martin, A.

To be published.

Macromolecule Content

Total Structure Weight: 1,211.82 kDa
Atom Count: 70,143
Modelled Residue Count: 8,842
Deposited Residue Count: 10,738
Unique protein chains: 27

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 12	A [auth W]	456	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O00232 (Homo sapiens) Explore O00232 Go to UniProtKB: O00232
PHAROS: O00232 GTEx: ENSG00000197170
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00232
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 8	B [auth C]	406	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62195 (Homo sapiens) Explore P62195 Go to UniProtKB: P62195
PHAROS: P62195 GTEx: ENSG00000087191
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62195
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 4	C [auth b]	377	Homo sapiens	Mutation(s): 0
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Find proteins for P55036 (Homo sapiens) Explore P55036 Go to UniProtKB: P55036
PHAROS: P55036 GTEx: ENSG00000159352
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55036
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 8	D [auth d]	350	Homo sapiens	Mutation(s): 0
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Find proteins for P48556 (Homo sapiens) Explore P48556 Go to UniProtKB: P48556
PHAROS: P48556 GTEx: ENSG00000099341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48556
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 2	E [auth f]	908	Homo sapiens	Mutation(s): 0
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Find proteins for Q13200 (Homo sapiens) Explore Q13200 Go to UniProtKB: Q13200
PHAROS: Q13200 GTEx: ENSG00000175166
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13200
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8 ultimate buster 1	F [auth g]	605	Homo sapiens	Mutation(s): 0 Gene Names: NUB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5A7 (Homo sapiens) Go to UniProtKB: Q9Y5A7
PHAROS: Q9Y5A7 GTEx: ENSG00000013374
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5A7-2
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 4	G [auth B]	440	Homo sapiens	Mutation(s): 0
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Find proteins for P62191 (Homo sapiens) Explore P62191 Go to UniProtKB: P62191
GTEx: ENSG00000100764
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62191
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 7	H [auth A]	433	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P35998 (Homo sapiens) Explore P35998 Go to UniProtKB: P35998
PHAROS: P35998 GTEx: ENSG00000161057
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35998
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6B	I [auth D]	418	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P43686 (Homo sapiens) Explore P43686 Go to UniProtKB: P43686
PHAROS: P43686 GTEx: ENSG00000013275
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43686
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 10B	J [auth E]	389	Homo sapiens	Mutation(s): 0
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Find proteins for P62333 (Homo sapiens) Explore P62333 Go to UniProtKB: P62333
GTEx: ENSG00000100519
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62333
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6A	K [auth F]	439	Homo sapiens	Mutation(s): 0
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Find proteins for P17980 (Homo sapiens) Explore P17980 Go to UniProtKB: P17980
PHAROS: P17980 GTEx: ENSG00000165916
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17980
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	L [auth G]	246	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens) Explore P60900 Go to UniProtKB: P60900
PHAROS: P60900 GTEx: ENSG00000100902
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60900
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	M [auth H]	234	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens) Explore P25787 Go to UniProtKB: P25787
PHAROS: P25787 GTEx: ENSG00000106588
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25787
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	N [auth I]	261	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens) Explore P25789 Go to UniProtKB: P25789
PHAROS: P25789 GTEx: ENSG00000041357
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25789
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-7	O [auth J]	248	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens) Explore O14818 Go to UniProtKB: O14818
PHAROS: O14818 GTEx: ENSG00000101182
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14818
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	P [auth K]	241	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens) Explore P28066 Go to UniProtKB: P28066
PHAROS: P28066 GTEx: ENSG00000143106
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28066
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	Q [auth L]	263	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens) Explore P25786 Go to UniProtKB: P25786
PHAROS: P25786 GTEx: ENSG00000129084
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25786
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	R [auth M]	255	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens) Explore P25788 Go to UniProtKB: P25788
PHAROS: P25788 GTEx: ENSG00000100567
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25788
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	S [auth O]	277	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens) Explore Q99436 Go to UniProtKB: Q99436
PHAROS: Q99436 GTEx: ENSG00000136930
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99436
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 1	T [auth U]	953	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q99460 (Homo sapiens) Explore Q99460 Go to UniProtKB: Q99460
PHAROS: Q99460 GTEx: ENSG00000173692
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99460
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 3	U [auth V]	534	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43242 (Homo sapiens) Explore O43242 Go to UniProtKB: O43242
PHAROS: O43242 GTEx: ENSG00000108344
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43242
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 14	V [auth c]	424	Homo sapiens	Mutation(s): 0 Gene Names: PSMD14 EC: 3.4.19
UniProt & NIH Common Fund Data Resources
Find proteins for O00487 (Homo sapiens) Explore O00487 Go to UniProtKB: O00487
PHAROS: O00487 GTEx: ENSG00000115233
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00487
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit SEM1	W [auth e]	70	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P60896 (Homo sapiens) Explore P60896 Go to UniProtKB: P60896
PHAROS: P60896 GTEx: ENSG00000127922
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60896
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 6	X [auth Y]	389	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15008 (Homo sapiens) Explore Q15008 Go to UniProtKB: Q15008
PHAROS: Q15008 GTEx: ENSG00000163636
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15008
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Reference Sequence

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 7	Y [auth Z]	324	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P51665 (Homo sapiens) Explore P51665 Go to UniProtKB: P51665
PHAROS: P51665 GTEx: ENSG00000103035
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51665
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Reference Sequence

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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 13	Z [auth a]	376	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNM6 (Homo sapiens) Explore Q9UNM6 Go to UniProtKB: Q9UNM6
PHAROS: Q9UNM6 GTEx: ENSG00000185627
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UNM6
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Reference Sequence

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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 11	AA [auth X]	422	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O00231 (Homo sapiens) Explore O00231 Go to UniProtKB: O00231
PHAROS: O00231 GTEx: ENSG00000108671
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00231
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain LA [auth F] SDF format, chain DA [auth B] SDF format, chain FA [auth A] SDF format, chain HA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain HA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain HA [auth D]	DA [auth B], FA [auth A], HA [auth D], JA [auth E], LA [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain DA [auth B] Focus chain FA [auth A] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain LA [auth F] Interactions & Density Focus chain DA [auth B] Focus chain FA [auth A] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain LA [auth F]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain BA [auth C]	BA [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain NA [auth c] MOL2 format, chain NA [auth c] mmCIF format, chain NA [auth c]	NA [auth c]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain NA [auth c] Interactions & Density Focus chain NA [auth c]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain MA [auth F] SDF format, chain CA [auth C] SDF format, chain EA [auth B] SDF format, chain GA [auth A] SDF format, chain KA [auth E] MOL2 format, chain IA [auth D] MOL2 format, chain MA [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain KA [auth E] mmCIF format, chain IA [auth D] mmCIF format, chain MA [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain KA [auth E]	CA [auth C] EA [auth B] GA [auth A] IA [auth D] KA [auth E] CA [auth C], EA [auth B], GA [auth A], IA [auth D], KA [auth E], MA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain EA [auth B] Focus chain GA [auth A] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain MA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain EA [auth B] Focus chain GA [auth A] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain MA [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

Arkinson, C.

Gee, C.L.

Martin, A.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-11-06
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Help and Resources

8USB

Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1

Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome

Entity ID: 1

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Sequence Annotations

Entity ID: 2

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Entity Groups

Sequence Annotations

Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Entity ID: 8

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19