8P4O

CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx

PDB DOI: https://doi.org/10.2210/pdb8P4O/pdb
EM Map EMD-17421: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3), Escherichia coli BL21
Mutation(s): No

Deposited: 2023-05-23 Released: 2024-07-03
Deposition Author(s): Wagner, J., Beck, F., Bracher, A., Caravajal, A.I., Wan, W., Bohn, S., Koerner, R., Baumeister, W., Fernandez-Busnadiego, R., Hartl, F.U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Visualizing chaperonin function in situ by cryo-electron tomography

Wagner, J., Caravajal, A.I., Beck, F., Bracher, A., Wan, W., Bohn, S., Koerner, R., Baumeister, W., Fernandez-Busnadiego, R., Hartl, F.U.

(2024) Nature

Macromolecule Content

Total Structure Weight: 519.52 kDa
Atom Count: 34,605
Modelled Residue Count: 4,712
Deposited Residue Count: 4,892
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	A, B, C, D, E A, B, C, D, E, F, G	547	Escherichia coli	Mutation(s): 0 Gene Names: groEL, groL, mopA, b4143, JW4103 EC: 5.6.1.7
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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Co-chaperonin GroES	H [auth O] I [auth P] J [auth Q] K [auth R] L [auth S] H [auth O], I [auth P], J [auth Q], K [auth R], L [auth S], M [auth T], N [auth U]	97	Escherichia coli	Mutation(s): 0 Gene Names: groES, groS, 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthase	O [auth 1]	384	Escherichia coli	Mutation(s): 0 Gene Names: metK, metX, b2942, JW2909 EC: 2.5.1.6
UniProt
Find proteins for P0A817 (Escherichia coli (strain K12)) Explore P0A817 Go to UniProtKB: P0A817
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain FA [auth E] SDF format, chain JA [auth F] SDF format, chain NA [auth G] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain X [auth C]	BA [auth D] FA [auth E] JA [auth F] NA [auth G] P [auth A] BA [auth D], FA [auth E], JA [auth F], NA [auth G], P [auth A], T [auth B], X [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth D] Focus chain FA [auth E] Focus chain JA [auth F] Focus chain NA [auth G] Focus chain P [auth A] Focus chain T [auth B] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain FA [auth E] Focus chain JA [auth F] Focus chain NA [auth G] Focus chain P [auth A] Focus chain T [auth B] Focus chain X [auth C]
BEF Query on BEF Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain LA [auth F] SDF format, chain PA [auth G] SDF format, chain R [auth A] SDF format, chain V [auth B] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain PA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C]	DA [auth D] HA [auth E] LA [auth F] PA [auth G] R [auth A] DA [auth D], HA [auth E], LA [auth F], PA [auth G], R [auth A], V [auth B], Z [auth C]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain DA [auth D] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain PA [auth G] Focus chain R [auth A] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain PA [auth G] Focus chain R [auth A] Focus chain V [auth B] Focus chain Z [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain IA [auth E] SDF format, chain MA [auth F] SDF format, chain QA [auth G] SDF format, chain S [auth A] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain QA [auth G] MOL2 format, chain S [auth A] MOL2 format, chain W [auth B]	AA [auth C] EA [auth D] IA [auth E] MA [auth F] QA [auth G] AA [auth C], EA [auth D], IA [auth E], MA [auth F], QA [auth G], S [auth A], W [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain MA [auth F] Focus chain QA [auth G] Focus chain S [auth A] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain MA [auth F] Focus chain QA [auth G] Focus chain S [auth A] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain GA [auth E] SDF format, chain KA [auth F] SDF format, chain OA [auth G] SDF format, chain Q [auth A] SDF format, chain U [auth B] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C]	CA [auth D] GA [auth E] KA [auth F] OA [auth G] Q [auth A] CA [auth D], GA [auth E], KA [auth F], OA [auth G], Q [auth A], U [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain OA [auth G] Focus chain Q [auth A] Focus chain U [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain OA [auth G] Focus chain Q [auth A] Focus chain U [auth B] Focus chain Y [auth C]