7PBX

Cryo-EM structure of the GroEL-GroES complex with ADP bound to both rings ("tight" conformation).

PDB DOI: https://doi.org/10.2210/pdb7PBX/pdb
EM Map EMD-13308: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli str. K-12 substr. W3110
Mutation(s): No

Deposited: 2021-08-02 Released: 2021-11-24
Deposition Author(s): Pichkur, E.B., Stanishneva-Konovalova, T.B.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.43 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Novel cryo-EM structure of an ADP-bound GroEL-GroES complex.

Kudryavtseva, S.S., Pichkur, E.B., Yaroshevich, I.A., Mamchur, A.A., Panina, I.S., Moiseenko, A.V., Sokolova, O.S., Muronetz, V.I., Stanishneva-Konovalova, T.B.

(2021) Sci Rep 11: 18241-18241

PubMed: 34521893 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-021-97657-x
Primary Citation of Related Structures:
7PBJ, 7PBX

PubMed Abstract:
The GroEL-GroES chaperonin complex is a bacterial protein folding system, functioning in an ATP-dependent manner. Upon ATP binding and hydrolysis, it undergoes multiple stages linked to substrate protein binding, folding and release. Structural methods helped to reveal several conformational states and provide more information about the chaperonin functional cycle. Here, using cryo-EM we resolved two nucleotide-bound structures of the bullet-shaped GroEL-GroES ₁ complex at 3.4 Å resolution. The main difference between them is the relative orientation of their apical domains. Both structures contain nucleotides in cis and trans GroEL rings; in contrast to previously reported bullet-shaped complexes where nucleotides were only present in the cis ring. Our results suggest that the bound nucleotides correspond to ADP, and that such a state appears at low ATP:ADP ratios.

Organizational Affiliation

Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.

Macromolecule Content

Total Structure Weight: 852.21 kDa
Atom Count: 59,472
Modelled Residue Count: 8,015
Deposited Residue Count: 8,015
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60 kDa chaperonin	A [auth Ac] B [auth Ad] D [auth Ai] E [auth Aj] G [auth Ao] A [auth Ac], B [auth Ad], D [auth Ai], E [auth Aj], G [auth Ao], H [auth Ap], J [auth Au], K [auth Av], M [auth Ba], N [auth Bb], P [auth Bg], Q [auth Bh], S [auth Bm], T [auth Bn]	524	Escherichia coli K-12	Mutation(s): 0 Gene Names: groL, groEL, mopA, b4143, JW4103
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5 Go to UniProtKB: P0A6F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6F5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
10 kDa chaperonin	C [auth Af] F [auth Al] I [auth Ar] L [auth Ax] O [auth Bd] C [auth Af], F [auth Al], I [auth Ar], L [auth Ax], O [auth Bd], R [auth Bj], U [auth Bp]	97	Escherichia coli K-12	Mutation(s): 0 Gene Names: groS, groES, mopB, b4142, JW4102
UniProt
Find proteins for P0A6F9 (Escherichia coli (strain K12)) Explore P0A6F9 Go to UniProtKB: P0A6F9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6F9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth Aj] SDF format, chain DA [auth Ao] SDF format, chain FA [auth Ap] SDF format, chain HA [auth Au] SDF format, chain JA [auth Av] SDF format, chain LA [auth Ba] SDF format, chain NA [auth Bb] SDF format, chain PA [auth Bg] SDF format, chain RA [auth Bh] SDF format, chain TA [auth Bm] SDF format, chain V [auth Ac] SDF format, chain VA [auth Bn] SDF format, chain X [auth Ad] SDF format, chain Z [auth Ai] MOL2 format, chain BA [auth Aj] MOL2 format, chain DA [auth Ao] MOL2 format, chain FA [auth Ap] MOL2 format, chain HA [auth Au] MOL2 format, chain JA [auth Av] MOL2 format, chain LA [auth Ba] MOL2 format, chain NA [auth Bb] MOL2 format, chain PA [auth Bg] MOL2 format, chain RA [auth Bh] MOL2 format, chain TA [auth Bm] MOL2 format, chain V [auth Ac] MOL2 format, chain VA [auth Bn] MOL2 format, chain X [auth Ad] MOL2 format, chain Z [auth Ai]	BA [auth Aj] DA [auth Ao] FA [auth Ap] HA [auth Au] JA [auth Av] BA [auth Aj], DA [auth Ao], FA [auth Ap], HA [auth Au], JA [auth Av], LA [auth Ba], NA [auth Bb], PA [auth Bg], RA [auth Bh], TA [auth Bm], V [auth Ac], VA [auth Bn], X [auth Ad], Z [auth Ai]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth Aj] Focus chain DA [auth Ao] Focus chain FA [auth Ap] Focus chain HA [auth Au] Focus chain JA [auth Av] Focus chain LA [auth Ba] Focus chain NA [auth Bb] Focus chain PA [auth Bg] Focus chain RA [auth Bh] Focus chain TA [auth Bm] Focus chain V [auth Ac] Focus chain VA [auth Bn] Focus chain X [auth Ad] Focus chain Z [auth Ai] Interactions & Density Focus chain BA [auth Aj] Focus chain DA [auth Ao] Focus chain FA [auth Ap] Focus chain HA [auth Au] Focus chain JA [auth Av] Focus chain LA [auth Ba] Focus chain NA [auth Bb] Focus chain PA [auth Bg] Focus chain RA [auth Bh] Focus chain TA [auth Bm] Focus chain V [auth Ac] Focus chain VA [auth Bn] Focus chain X [auth Ad] Focus chain Z [auth Ai]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth Ai] SDF format, chain GA [auth Ap] SDF format, chain IA [auth Au] SDF format, chain KA [auth Av] SDF format, chain MA [auth Ba] SDF format, chain QA [auth Bg] SDF format, chain SA [auth Bh] SDF format, chain UA [auth Bm] SDF format, chain W [auth Ac] SDF format, chain WA [auth Bn] SDF format, chain Y [auth Ad] SDF format, chain CA [auth Aj] SDF format, chain EA [auth Ao] SDF format, chain OA [auth Bb] MOL2 format, chain AA [auth Ai] MOL2 format, chain GA [auth Ap] MOL2 format, chain IA [auth Au] MOL2 format, chain KA [auth Av] MOL2 format, chain MA [auth Ba] MOL2 format, chain QA [auth Bg] MOL2 format, chain SA [auth Bh] MOL2 format, chain UA [auth Bm] MOL2 format, chain W [auth Ac] MOL2 format, chain WA [auth Bn] MOL2 format, chain Y [auth Ad] MOL2 format, chain CA [auth Aj] MOL2 format, chain EA [auth Ao] MOL2 format, chain OA [auth Bb]	AA [auth Ai] CA [auth Aj] EA [auth Ao] GA [auth Ap] IA [auth Au] AA [auth Ai], CA [auth Aj], EA [auth Ao], GA [auth Ap], IA [auth Au], KA [auth Av], MA [auth Ba], OA [auth Bb], QA [auth Bg], SA [auth Bh], UA [auth Bm], W [auth Ac], WA [auth Bn], Y [auth Ad]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth Ai] Focus chain CA [auth Aj] Focus chain EA [auth Ao] Focus chain GA [auth Ap] Focus chain IA [auth Au] Focus chain KA [auth Av] Focus chain MA [auth Ba] Focus chain OA [auth Bb] Focus chain QA [auth Bg] Focus chain SA [auth Bh] Focus chain UA [auth Bm] Focus chain W [auth Ac] Focus chain WA [auth Bn] Focus chain Y [auth Ad] Interactions & Density Focus chain AA [auth Ai] Focus chain CA [auth Aj] Focus chain EA [auth Ao] Focus chain GA [auth Ap] Focus chain IA [auth Au] Focus chain KA [auth Av] Focus chain MA [auth Ba] Focus chain OA [auth Bb] Focus chain QA [auth Bg] Focus chain SA [auth Bh] Focus chain UA [auth Bm] Focus chain W [auth Ac] Focus chain WA [auth Bn] Focus chain Y [auth Ad]