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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "UBI1"

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Search Summary

This query matches 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Saccharomyces cerevisiae (10)
	Saccharomyces cerevisiae S288C (5)
	Chromobacterium violaceum ATCC 12472 (2)
	Homo sapiens (2)
	Rattus norvegicus (1)

Taxonomy

	Eukaryota (16)
	Bacteria (2)

Experimental Method

	SOLUTION NMR (6)
	ELECTRON MICROSCOPY (5)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

	Protein (16)
	RNA (3)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (1)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)
	3.5 - 4.0 (4)
	4.0 - 4.5 (2)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (5)
	2010 - 2014 (1)
	2015 - 2019 (5)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (4)
	Ligases (1)
	Transferases (2)

Symmetry Type

Asymmetric (16)

SCOP Classification

	Alpha and beta proteins (a+b) (7)
	Artifacts (2)
	All alpha proteins (2)
	All beta proteins (1)

AllSelected

1 to 16 of 16 Structures

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1OTR \| pdb_00001otr	Download File View File

Solution Structure of a CUE-Ubiquitin Complex

Kang, R.S., Daniels, C.M., Salerno, W.J., Radhakrishnan, I.

(2003) Cell 113: 621-630

Released	2003-06-24
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Ubiquitin (protein) protein Cue2 (protein)

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1ZW7 \| pdb_00001zw7	Download File View File

Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences

Ermolenko, D.N., Dangi, B., Gronenborn, A.M., Makhatadze, G.I.

(2007) Biophys Chem 126: 25-35

Released	2006-05-16
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Ubiquitin (protein)

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2JT4 \| pdb_00002jt4	Download File View File

Solution Structure of the Sla1 SH3-3-Ubiquitin Complex

He, Y., Radhakrishnan, I.

(2007) J Mol Biology 373: 190-196

Released	2007-09-25
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Cytoskeleton assembly control protein SLA1 (protein) Ubiquitin (protein)

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2JWZ \| pdb_00002jwz	Download File View File

Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins

Haririnia, A., Verma, R., Purohit, N., Twarog, M., Deshaies, R., Bolon, D., Fushman, D.

(2008) J Mol Biology 375: 979-996

Released	2008-01-08
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	Ubiquitin (protein)

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2JY6 \| pdb_00002jy6	Download File View File

Solution structure of the complex of ubiquitin and ubiquilin 1 UBA domain

Zhang, D., Raasi, S., Fushman, D.

(2008) J Mol Biology 377: 162-180

Released	2008-03-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ubiquilin-1 (protein) Ubiquitin protein (protein)

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2L00 \| pdb_00002l00	Download File View File

Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin

Garner, T.P., Long, J.E., Searle, M.S., Layfield, R.

To be published

Released	2011-07-20
Method	SOLUTION NMR
Organisms	Rattus norvegicus Saccharomyces cerevisiae
Macromolecule	Ubiquitin (protein) Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a) (protein)
Unique Ligands	ZN

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3CMM \| pdb_00003cmm	Download File View File

Crystal Structure of the Uba1-Ubiquitin Complex

Lee, I., Schindelin, H.

(2008) Cell 134: 268-278

Released	2008-08-05
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Ubiquitin (protein) Ubiquitin-activating enzyme E1 1 (protein)
Unique Ligands	PRO

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5MEI \| pdb_00005mei	Download File View File

Crystal structure of Agelastatin A bound to the 80S ribosome

McClary, B., Zinshteyn, B., Meyer, M., Jouanneau, M., Pellegrino, S., Yusupova, G., Schuller, A., Reyes, J.C.P., Lu, J., Luo, C., Dang, Y., Romo, D., Yusupov, M., Green, R., Liu, J.O.

(2017) Cell Chem Biol 24: 605-613.e5

Released	2017-06-28
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 79 Unique nucleic acid chains: 4
Unique Ligands	7MB, MG, OHX, ZN

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5TBW \| pdb_00005tbw	Download File View File

Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome

Konst, Z.A., Szklarski, A.R., Pellegrino, S., Michalak, S.E., Meyer, M., Zanette, C., Cencic, R., Nam, S., Horne, D.A., Pelletier, J., Mobley, D.L., Yusupova, G., Yusupov, M., Vanderwal, C.D.

(2017) Nat Chem 9: 1140-1149

Released	2017-07-26
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 79 Unique nucleic acid chains: 4
Unique Ligands	7AL, MG, OHX, ZN

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6EF3 \| pdb_00006ef3	Download File View File

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)

de la Pena, A.H., Goodall, E.A., Gates, S.N., Lander, G.C., Martin, A.

(2018) Science 362:

Released	2018-10-17
Method	ELECTRON MICROSCOPY 4.17 Å
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 24
Unique Ligands	ADP, ATP

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6OA9 \| pdb_00006oa9	Download File View File

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

Twomey, E.C., Ji, Z., Wales, T.E., Bodnar, N.O., Engen, J.R., Rapoport, T.A.

(2019) Science 365:

Released	2019-07-03
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 48 (protein) Nuclear protein localization protein 4 (protein) Ubiquitin (protein)
Unique Ligands	ADP, ATP, ZN

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6OAA \| pdb_00006oaa	Download File View File

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1

Twomey, E.C., Ji, Z., Wales, T.E., Bodnar, N.O., Engen, J.R., Rapoport, T.A.

(2019) Science 365:

Released	2019-07-03
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 48 (protein) Nuclear protein localization protein 4 (protein) Ubiquitin (protein)
Unique Ligands	ADP, BEF

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6OIG \| pdb_00006oig	Download File View File

Subunit joining exposes nascent pre-40S rRNA for processing and quality control

Rai, J., Parker, M.D., Ghalei, H., Johnson, M.C., Karbstein, K., Stroupe, M.E.

(2021) RNA 27: 221-233

Released	2020-09-30
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 45 Unique nucleic acid chains: 3

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8DAS \| pdb_00008das	Download File View File

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA)

Lee, H.G., Lima, C.D.

(2023) Proc Natl Acad Sci U S A 120: e2213703120-e2213703120

Released	2022-11-30
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Cell division control protein 48 (protein) Nuclear protein localization protein 4 (protein) Ubiquitin (protein) Ubiquitin fusion degradation protein 1 (protein)
Unique Ligands	ADP, ATP, ZN

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8HTD \| pdb_00008htd	Download File View File

Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin

Tan, J., Wang, X., Zhou, Y., Zhu, Y.

(2024) Nat Chem Biol 20: 463-472

Released	2023-11-22
Method	X-RAY DIFFRACTION 1.848 Å
Organisms	Chromobacterium violaceum ATCC 12472 Saccharomyces cerevisiae S288C
Macromolecule	NAD(+)--protein-threonine ADP-ribosyltransferase (protein) Ubiquitin (protein)

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8HTE \| pdb_00008hte	Download File View File

Crystal structure of an effector mutant in complex with ubiquitin

Tan, J., Wang, X., Zhou, Y., Zhu, Y.

(2024) Nat Chem Biol 20: 463-472

Released	2023-11-22
Method	X-RAY DIFFRACTION 2.307 Å
Organisms	Chromobacterium violaceum ATCC 12472 Saccharomyces cerevisiae S288C
Macromolecule	NAD(+)--protein-threonine ADP-ribosyltransferase (protein) Ubiquitin (protein)
Unique Ligands	AR6, GOL, NCA, SO4

1 to 16 of 16 Structures

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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.

1OTR | pdb_00001otr

Solution Structure of a CUE-Ubiquitin Complex

1ZW7 | pdb_00001zw7

Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences

2JT4 | pdb_00002jt4

Solution Structure of the Sla1 SH3-3-Ubiquitin Complex

2JWZ | pdb_00002jwz

Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins

2JY6 | pdb_00002jy6

Solution structure of the complex of ubiquitin and ubiquilin 1 UBA domain

2L00 | pdb_00002l00

Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin

3CMM | pdb_00003cmm

Crystal Structure of the Uba1-Ubiquitin Complex

5MEI | pdb_00005mei

Crystal structure of Agelastatin A bound to the 80S ribosome

5TBW | pdb_00005tbw

Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome

6EF3 | pdb_00006ef3

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)

6OA9 | pdb_00006oa9

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

6OAA | pdb_00006oaa

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1

6OIG | pdb_00006oig

Subunit joining exposes nascent pre-40S rRNA for processing and quality control

8DAS | pdb_00008das

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA)

8HTD | pdb_00008htd

Crystal structure of an effector from Chromobacterium violaceum in complex with ubiquitin

8HTE | pdb_00008hte

Crystal structure of an effector mutant in complex with ubiquitin

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1OTR | pdb_00001otr

1ZW7 | pdb_00001zw7

2JT4 | pdb_00002jt4

2JWZ | pdb_00002jwz

2JY6 | pdb_00002jy6

2L00 | pdb_00002l00

3CMM | pdb_00003cmm

5MEI | pdb_00005mei

5TBW | pdb_00005tbw

6EF3 | pdb_00006ef3

6OA9 | pdb_00006oa9

6OAA | pdb_00006oaa

6OIG | pdb_00006oig

8DAS | pdb_00008das

8HTD | pdb_00008htd

8HTE | pdb_00008hte