3WVL | pdb_00003wvl

Crystal structure of the football-shaped GroEL-GroES complex (GroEL: GroES2:ATP14) from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb3WVL/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-05-23 Released: 2014-09-17
Deposition Author(s): Koike-Takeshita, A., Arakawa, T., Taguchi, H., Shimamura, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.79 Å
R-Value Free:
0.250 (Depositor), 0.227 (DCC)
R-Value Work:
0.211 (Depositor), 0.219 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a symmetric football-shaped GroEL:GroES2-ATP14 complex determined at 3.8 angstrom reveals rearrangement between two GroEL rings.

Koike-Takeshita, A., Arakawa, T., Taguchi, H., Shimamura, T.

(2014) J Mol Biology 426: 3634-3641

PubMed: 25174333 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2014.08.017
Primary Citation Related Structures:
3WVL

PubMed Abstract:
The chaperonin GroEL is an essential chaperone that assists in protein folding with the aid of GroES and ATP. GroEL forms a double-ring structure, and both rings can bind GroES in the presence of ATP. Recent progress on the GroEL mechanism has revealed the importance of a symmetric 1:2 GroEL:GroES2 complex (the "football"-shaped complex) as a critical intermediate during the functional GroEL cycle. We determined the crystal structure of the football GroEL:GroES2-ATP14 complex from Escherichia coli at 3.8Å, using a GroEL mutant that is extremely defective in ATP hydrolysis. The overall structure of the football complex resembled the GroES-bound GroEL ring of the asymmetric 1:1 GroEL:GroES complex (the "bullet" complex). However, the two GroES-bound GroEL rings form a modified interface by an ~7° rotation about the 7-fold axis. As a result, the inter-ring contacts between the two GroEL rings in the football complex differed from those in the bullet complex. The differences provide a structural basis for the apparently impaired inter-ring negative cooperativity observed in several biochemical analyses.

Organizational Affiliation

Department of Applied Bioscience, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan.

Macromolecule Content

Total Structure Weight: 955.85 kDa
Atom Count: 64,540
Modeled Residue Count: 8,694
Deposited Residue Count: 9,030
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60 kDa chaperonin	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	548	Escherichia coli K-12	Mutation(s): 2 Gene Names: groL, groEL, mopA, b4143, JW4103 EC: 3.6.4.9 (PDB Primary Data), 5.6.1.7 (UniProt)
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5 Go to UniProtKB: P0A6F5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6F5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
10 kDa chaperonin	AA [auth a] BA [auth b] O P Q AA [auth a], BA [auth b], O, P, Q, R, S, T, U, V, W, X, Y, Z	97	Escherichia coli K-12	Mutation(s): 0 Gene Names: groS, groES, mopB, b4142, JW4102 EC: 3.6.4.9
UniProt
Find proteins for P0A6F9 (Escherichia coli (strain K12)) Explore P0A6F9 Go to UniProtKB: P0A6F9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6F9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain CA [auth A] SDF format, chain DB [auth J] SDF format, chain FA [auth B] SDF format, chain GB [auth K] SDF format, chain IA [auth C] SDF format, chain JB [auth L] SDF format, chain LA [auth D] SDF format, chain MB [auth M] SDF format, chain OA [auth E] SDF format, chain PB [auth N] SDF format, chain RA [auth F] SDF format, chain UA [auth G] SDF format, chain XA [auth H] MOL2 format, chain AB [auth I] MOL2 format, chain CA [auth A] MOL2 format, chain DB [auth J] MOL2 format, chain FA [auth B] MOL2 format, chain GB [auth K] MOL2 format, chain IA [auth C] MOL2 format, chain JB [auth L] MOL2 format, chain LA [auth D] MOL2 format, chain MB [auth M] MOL2 format, chain OA [auth E] MOL2 format, chain PB [auth N] MOL2 format, chain RA [auth F] MOL2 format, chain UA [auth G] MOL2 format, chain XA [auth H] mmCIF format, chain AB [auth I] mmCIF format, chain CA [auth A] mmCIF format, chain DB [auth J] mmCIF format, chain FA [auth B] mmCIF format, chain GB [auth K] mmCIF format, chain IA [auth C] mmCIF format, chain JB [auth L] mmCIF format, chain LA [auth D] mmCIF format, chain MB [auth M] mmCIF format, chain OA [auth E] mmCIF format, chain PB [auth N] mmCIF format, chain RA [auth F] mmCIF format, chain UA [auth G] mmCIF format, chain XA [auth H]	AB [auth I] CA [auth A] DB [auth J] FA [auth B] GB [auth K] AB [auth I], CA [auth A], DB [auth J], FA [auth B], GB [auth K], IA [auth C], JB [auth L], LA [auth D], MB [auth M], OA [auth E], PB [auth N], RA [auth F], UA [auth G], XA [auth H]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AB [auth I] Focus chain CA [auth A] Focus chain DB [auth J] Focus chain FA [auth B] Focus chain GB [auth K] Focus chain IA [auth C] Focus chain JB [auth L] Focus chain LA [auth D] Focus chain MB [auth M] Focus chain OA [auth E] Focus chain PB [auth N] Focus chain RA [auth F] Focus chain UA [auth G] Focus chain XA [auth H] Interactions & Density Focus chain AB [auth I] Focus chain CA [auth A] Focus chain DB [auth J] Focus chain FA [auth B] Focus chain GB [auth K] Focus chain IA [auth C] Focus chain JB [auth L] Focus chain LA [auth D] Focus chain MB [auth M] Focus chain OA [auth E] Focus chain PB [auth N] Focus chain RA [auth F] Focus chain UA [auth G] Focus chain XA [auth H]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain CB [auth I] SDF format, chain EA [auth A] SDF format, chain FB [auth J] SDF format, chain HA [auth B] SDF format, chain IB [auth K] SDF format, chain KA [auth C] SDF format, chain LB [auth L] SDF format, chain NA [auth D] SDF format, chain OB [auth M] SDF format, chain QA [auth E] SDF format, chain RB [auth N] SDF format, chain TA [auth F] SDF format, chain WA [auth G] SDF format, chain ZA [auth H] MOL2 format, chain CB [auth I] MOL2 format, chain EA [auth A] MOL2 format, chain FB [auth J] MOL2 format, chain HA [auth B] MOL2 format, chain IB [auth K] MOL2 format, chain KA [auth C] MOL2 format, chain LB [auth L] MOL2 format, chain NA [auth D] MOL2 format, chain OB [auth M] MOL2 format, chain QA [auth E] MOL2 format, chain RB [auth N] MOL2 format, chain TA [auth F] MOL2 format, chain WA [auth G] MOL2 format, chain ZA [auth H] mmCIF format, chain CB [auth I] mmCIF format, chain EA [auth A] mmCIF format, chain FB [auth J] mmCIF format, chain HA [auth B] mmCIF format, chain IB [auth K] mmCIF format, chain KA [auth C] mmCIF format, chain LB [auth L] mmCIF format, chain NA [auth D] mmCIF format, chain OB [auth M] mmCIF format, chain QA [auth E] mmCIF format, chain RB [auth N] mmCIF format, chain TA [auth F] mmCIF format, chain WA [auth G] mmCIF format, chain ZA [auth H]	CB [auth I] EA [auth A] FB [auth J] HA [auth B] IB [auth K] CB [auth I], EA [auth A], FB [auth J], HA [auth B], IB [auth K], KA [auth C], LB [auth L], NA [auth D], OB [auth M], QA [auth E], RB [auth N], TA [auth F], WA [auth G], ZA [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CB [auth I] Focus chain EA [auth A] Focus chain FB [auth J] Focus chain HA [auth B] Focus chain IB [auth K] Focus chain KA [auth C] Focus chain LB [auth L] Focus chain NA [auth D] Focus chain OB [auth M] Focus chain QA [auth E] Focus chain RB [auth N] Focus chain TA [auth F] Focus chain WA [auth G] Focus chain ZA [auth H] Interactions & Density Focus chain CB [auth I] Focus chain EA [auth A] Focus chain FB [auth J] Focus chain HA [auth B] Focus chain IB [auth K] Focus chain KA [auth C] Focus chain LB [auth L] Focus chain NA [auth D] Focus chain OB [auth M] Focus chain QA [auth E] Focus chain RB [auth N] Focus chain TA [auth F] Focus chain WA [auth G] Focus chain ZA [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BB [auth I] SDF format, chain DA [auth A] SDF format, chain EB [auth J] SDF format, chain GA [auth B] SDF format, chain HB [auth K] SDF format, chain JA [auth C] SDF format, chain KB [auth L] SDF format, chain MA [auth D] SDF format, chain NB [auth M] SDF format, chain PA [auth E] SDF format, chain QB [auth N] SDF format, chain SA [auth F] SDF format, chain VA [auth G] SDF format, chain YA [auth H] MOL2 format, chain BB [auth I] MOL2 format, chain DA [auth A] MOL2 format, chain EB [auth J] MOL2 format, chain GA [auth B] MOL2 format, chain HB [auth K] MOL2 format, chain JA [auth C] MOL2 format, chain KB [auth L] MOL2 format, chain MA [auth D] MOL2 format, chain NB [auth M] MOL2 format, chain PA [auth E] MOL2 format, chain QB [auth N] MOL2 format, chain SA [auth F] MOL2 format, chain VA [auth G] MOL2 format, chain YA [auth H] mmCIF format, chain BB [auth I] mmCIF format, chain DA [auth A] mmCIF format, chain EB [auth J] mmCIF format, chain GA [auth B] mmCIF format, chain HB [auth K] mmCIF format, chain JA [auth C] mmCIF format, chain KB [auth L] mmCIF format, chain MA [auth D] mmCIF format, chain NB [auth M] mmCIF format, chain PA [auth E] mmCIF format, chain QB [auth N] mmCIF format, chain SA [auth F] mmCIF format, chain VA [auth G] mmCIF format, chain YA [auth H]	BB [auth I] DA [auth A] EB [auth J] GA [auth B] HB [auth K] BB [auth I], DA [auth A], EB [auth J], GA [auth B], HB [auth K], JA [auth C], KB [auth L], MA [auth D], NB [auth M], PA [auth E], QB [auth N], SA [auth F], VA [auth G], YA [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth I] Focus chain DA [auth A] Focus chain EB [auth J] Focus chain GA [auth B] Focus chain HB [auth K] Focus chain JA [auth C] Focus chain KB [auth L] Focus chain MA [auth D] Focus chain NB [auth M] Focus chain PA [auth E] Focus chain QB [auth N] Focus chain SA [auth F] Focus chain VA [auth G] Focus chain YA [auth H] Interactions & Density Focus chain BB [auth I] Focus chain DA [auth A] Focus chain EB [auth J] Focus chain GA [auth B] Focus chain HB [auth K] Focus chain JA [auth C] Focus chain KB [auth L] Focus chain MA [auth D] Focus chain NB [auth M] Focus chain PA [auth E] Focus chain QB [auth N] Focus chain SA [auth F] Focus chain VA [auth G] Focus chain YA [auth H]