8BAA

CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II.

PDB DOI: https://doi.org/10.2210/pdb8BAA/pdb
EM Map EMD-15944: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Escherichia coli K-12, Rhodospirillum rubrum ATCC 11170
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-11 Released: 2025-02-12
Deposition Author(s): Gardner, S., Saibil, H.R.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 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

CryoEM snapshots of non-native Rubisco bound to GroEL, GroEL-ADP.BeF3, and GroEL-GroES.

Gardner, S., Lukyanova, N., Darrow, M.C., Thalassinos, K., Saibil, H.R.

To be published.

Macromolecule Content

Total Structure Weight: 932.18 kDa
Atom Count: 62,925
Modelled Residue Count: 8,467
Deposited Residue Count: 8,803
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, H, I, J, K, L, M, N	547	Escherichia coli K-12	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 LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Co-chaperonin GroES	O, P, Q, R, S O, P, Q, R, S, T, U	97	Escherichia coli K-12	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 LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase	V [auth Z]	466	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Gene Names: cbbM, Rru_A2400 EC: 4.1.1.39
UniProt
Find proteins for Q2RRP5 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RRP5 Go to UniProtKB: Q2RRP5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RRP5
Sequence Annotations Expand
Reference Sequence LOADING

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 B] SDF format, chain EA [auth C] SDF format, chain FA [auth D] SDF format, chain FB [auth L] SDF format, chain IB [auth M] SDF format, chain JB [auth N] SDF format, chain KA [auth E] SDF format, chain PA [auth G] SDF format, chain SA [auth H] SDF format, chain XA [auth J] SDF format, chain Y [auth A] SDF format, chain BB [auth K] SDF format, chain NA [auth F] SDF format, chain VA [auth I] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth L] MOL2 format, chain IB [auth M] MOL2 format, chain JB [auth N] MOL2 format, chain KA [auth E] MOL2 format, chain PA [auth G] MOL2 format, chain SA [auth H] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth A] MOL2 format, chain BB [auth K] MOL2 format, chain NA [auth F] MOL2 format, chain VA [auth I] mmCIF format, chain BA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain FB [auth L] mmCIF format, chain IB [auth M] mmCIF format, chain JB [auth N] mmCIF format, chain KA [auth E] mmCIF format, chain PA [auth G] mmCIF format, chain SA [auth H] mmCIF format, chain XA [auth J] mmCIF format, chain Y [auth A] mmCIF format, chain BB [auth K] mmCIF format, chain NA [auth F] mmCIF format, chain VA [auth I]	BA [auth B] BB [auth K] EA [auth C] FA [auth D] FB [auth L] BA [auth B], BB [auth K], EA [auth C], FA [auth D], FB [auth L], IB [auth M], JB [auth N], KA [auth E], NA [auth F], PA [auth G], SA [auth H], VA [auth I], XA [auth J], Y [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth B] Focus chain BB [auth K] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain FB [auth L] Focus chain IB [auth M] Focus chain JB [auth N] Focus chain KA [auth E] Focus chain NA [auth F] Focus chain PA [auth G] Focus chain SA [auth H] Focus chain VA [auth I] Focus chain XA [auth J] Focus chain Y [auth A] Interactions & Density Focus chain BA [auth B] Focus chain BB [auth K] Focus chain EA [auth C] Focus chain FA [auth D] Focus chain FB [auth L] Focus chain IB [auth M] Focus chain JB [auth N] Focus chain KA [auth E] Focus chain NA [auth F] Focus chain PA [auth G] Focus chain SA [auth H] Focus chain VA [auth I] Focus chain XA [auth J] Focus chain Y [auth A]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain GA [auth D] SDF format, chain IA [auth E] SDF format, chain LA [auth F] SDF format, chain OA [auth G] SDF format, chain W [auth A] SDF format, chain DA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain W [auth A] MOL2 format, chain DA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain OA [auth G] mmCIF format, chain W [auth A] mmCIF format, chain DA [auth C]	AA [auth B] DA [auth C] GA [auth D] IA [auth E] LA [auth F] AA [auth B], DA [auth C], GA [auth D], IA [auth E], LA [auth F], OA [auth G], W [auth A]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain AA [auth B] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain OA [auth G] Focus chain W [auth A] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain OA [auth G] Focus chain W [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain DB [auth L] SDF format, chain HB [auth M] SDF format, chain KB [auth N] SDF format, chain TA [auth H] SDF format, chain YA [auth J] SDF format, chain WA [auth I] MOL2 format, chain AB [auth K] MOL2 format, chain DB [auth L] MOL2 format, chain HB [auth M] MOL2 format, chain KB [auth N] MOL2 format, chain TA [auth H] MOL2 format, chain YA [auth J] MOL2 format, chain WA [auth I] mmCIF format, chain AB [auth K] mmCIF format, chain DB [auth L] mmCIF format, chain HB [auth M] mmCIF format, chain KB [auth N] mmCIF format, chain TA [auth H] mmCIF format, chain YA [auth J] mmCIF format, chain WA [auth I]	AB [auth K] DB [auth L] HB [auth M] KB [auth N] TA [auth H] AB [auth K], DB [auth L], HB [auth M], KB [auth N], TA [auth H], WA [auth I], YA [auth J]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain DB [auth L] Focus chain HB [auth M] Focus chain KB [auth N] Focus chain TA [auth H] Focus chain WA [auth I] Focus chain YA [auth J] Interactions & Density Focus chain AB [auth K] Focus chain DB [auth L] Focus chain HB [auth M] Focus chain KB [auth N] Focus chain TA [auth H] Focus chain WA [auth I] Focus chain YA [auth J]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain EB [auth L] SDF format, chain GB [auth M] SDF format, chain HA [auth D] SDF format, chain JA [auth E] SDF format, chain LB [auth N] SDF format, chain MA [auth F] SDF format, chain QA [auth G] SDF format, chain RA [auth H] SDF format, chain UA [auth I] SDF format, chain X [auth A] SDF format, chain ZA [auth J] SDF format, chain CA [auth C] SDF format, chain CB [auth K] SDF format, chain Z [auth B] MOL2 format, chain EB [auth L] MOL2 format, chain GB [auth M] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain LB [auth N] MOL2 format, chain MA [auth F] MOL2 format, chain QA [auth G] MOL2 format, chain RA [auth H] MOL2 format, chain UA [auth I] MOL2 format, chain X [auth A] MOL2 format, chain ZA [auth J] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth K] MOL2 format, chain Z [auth B] mmCIF format, chain EB [auth L] mmCIF format, chain GB [auth M] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain LB [auth N] mmCIF format, chain MA [auth F] mmCIF format, chain QA [auth G] mmCIF format, chain RA [auth H] mmCIF format, chain UA [auth I] mmCIF format, chain X [auth A] mmCIF format, chain ZA [auth J] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth K] mmCIF format, chain Z [auth B]	CA [auth C] CB [auth K] EB [auth L] GB [auth M] HA [auth D] CA [auth C], CB [auth K], EB [auth L], GB [auth M], HA [auth D], JA [auth E], LB [auth N], MA [auth F], QA [auth G], RA [auth H], UA [auth I], X [auth A], Z [auth B], ZA [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain CB [auth K] Focus chain EB [auth L] Focus chain GB [auth M] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain LB [auth N] Focus chain MA [auth F] Focus chain QA [auth G] Focus chain RA [auth H] Focus chain UA [auth I] Focus chain X [auth A] Focus chain Z [auth B] Focus chain ZA [auth J] Interactions & Density Focus chain CA [auth C] Focus chain CB [auth K] Focus chain EB [auth L] Focus chain GB [auth M] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain LB [auth N] Focus chain MA [auth F] Focus chain QA [auth G] Focus chain RA [auth H] Focus chain UA [auth I] Focus chain X [auth A] Focus chain Z [auth B] Focus chain ZA [auth J]