9CPK | pdb_00009cpk

D8 symmetry reconstruction of MmCPn in closed state

PDB DOI: https://doi.org/10.2210/pdb9CPK/pdb
EM Map EMD-45793: EMDB EMDataResource

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

Deposited: 2024-07-18 Released: 2025-07-30
Deposition Author(s): Yanyan, Z.
Funding Organization(s): Other private, Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

wwPDB Validation 3D Report Full Report

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

Literature

Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution.

Zhao, Y., Schmid, M.F., Chiu, W.

(2025) Structure 33: 372-380.e2

PubMed: 39644888 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.str.2024.11.008
Primary Citation of Related Structures:
9CPK

PubMed Abstract:
Cryogenic electron microscopy single particle analysis (cryoEM-SPA) has evolved into a routine approach for determining macromolecule structures to near-atomic resolution. Cryogenic electron tomography subtomogram averaging (cryoET-STA) toward a similar resolution, in contrast, is still under active development. Here, we use the archeal chaperonin MmCpn as a model macromolecule to quantitatively investigate the resolution limiting factors of cryoET-STA in terms of cumulative electron dose, ice thickness, subtomogram numbers, and tilt angle ranges. By delineating the feasibility and experimental factors of attaining near atomic resolution structure with cryoET-STA, especially the effect of electron damage through the tilt series and inelastic scattering at various ice thickness, we encourage a customized tilt series collection strategy for efficient throughput. This study provides a biophysical basis for the application of cryoET-STA (for highly symmetric molecules like MmCpn) toward high resolution and the rationales in using cryoET-STA to achieve an efficient outcome at the desired resolution.

Organizational Affiliation

Department of Bioengineering, James Clark Center, Stanford University, Stanford, CA 94305, USA. Electronic address: yanyanz@stanford.edu.

Macromolecule Content

Total Structure Weight: 941.84 kDa
Atom Count: 62,256
Modeled Residue Count: 8,208
Deposited Residue Count: 8,688
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin	A [auth B] B [auth J] C [auth K] D [auth L] E [auth M] A [auth B], B [auth J], C [auth K], D [auth L], E [auth M], F [auth A], G [auth C], H [auth D], I [auth N], J [auth E], K [auth F], L [auth G], M [auth H], N [auth I], O, P	543	Methanococcus maripaludis	Mutation(s): 0
UniProt
Find proteins for Q6LX38 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL)) Explore Q6LX38 Go to UniProtKB: Q6LX38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6LX38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 ZB [auth P] SDF format, chain Z [auth K] SDF format, chain XA [auth N] SDF format, chain VB [auth O] SDF format, chain V [auth J] SDF format, chain TA [auth D] SDF format, chain RB [auth I] SDF format, chain R [auth B] SDF format, chain PA [auth C] SDF format, chain NB [auth H] SDF format, chain LA [auth A] SDF format, chain JB [auth G] SDF format, chain HA [auth M] SDF format, chain FB [auth F] SDF format, chain DA [auth L] SDF format, chain BB [auth E] MOL2 format, chain ZB [auth P] MOL2 format, chain Z [auth K] MOL2 format, chain XA [auth N] MOL2 format, chain VB [auth O] MOL2 format, chain V [auth J] MOL2 format, chain TA [auth D] MOL2 format, chain RB [auth I] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain NB [auth H] MOL2 format, chain LA [auth A] MOL2 format, chain JB [auth G] MOL2 format, chain HA [auth M] MOL2 format, chain FB [auth F] MOL2 format, chain DA [auth L] MOL2 format, chain BB [auth E] mmCIF format, chain ZB [auth P] mmCIF format, chain Z [auth K] mmCIF format, chain XA [auth N] mmCIF format, chain VB [auth O] mmCIF format, chain V [auth J] mmCIF format, chain TA [auth D] mmCIF format, chain RB [auth I] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain NB [auth H] mmCIF format, chain LA [auth A] mmCIF format, chain JB [auth G] mmCIF format, chain HA [auth M] mmCIF format, chain FB [auth F] mmCIF format, chain DA [auth L] mmCIF format, chain BB [auth E]	BB [auth E] DA [auth L] FB [auth F] HA [auth M] JB [auth G] BB [auth E], DA [auth L], FB [auth F], HA [auth M], JB [auth G], LA [auth A], NB [auth H], PA [auth C], R [auth B], RB [auth I], TA [auth D], V [auth J], VB [auth O], XA [auth N], Z [auth K], ZB [auth P]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BB [auth E] Focus chain DA [auth L] Focus chain FB [auth F] Focus chain HA [auth M] Focus chain JB [auth G] Focus chain LA [auth A] Focus chain NB [auth H] Focus chain PA [auth C] Focus chain R [auth B] Focus chain RB [auth I] Focus chain TA [auth D] Focus chain V [auth J] Focus chain VB [auth O] Focus chain XA [auth N] Focus chain Z [auth K] Focus chain ZB [auth P] Interactions & Density Focus chain BB [auth E] Focus chain DA [auth L] Focus chain FB [auth F] Focus chain HA [auth M] Focus chain JB [auth G] Focus chain LA [auth A] Focus chain NB [auth H] Focus chain PA [auth C] Focus chain R [auth B] Focus chain RB [auth I] Focus chain TA [auth D] Focus chain V [auth J] Focus chain VB [auth O] Focus chain XA [auth N] Focus chain Z [auth K] Focus chain ZB [auth P]
AF3 (Subject of Investigation/LOI) Query on AF3 Download Ideal Coordinates CCD File SDF format, chain YA [auth N] SDF format, chain WB [auth O] SDF format, chain W [auth J] SDF format, chain UA [auth D] SDF format, chain SB [auth I] SDF format, chain S [auth B] SDF format, chain QA [auth C] SDF format, chain OB [auth H] SDF format, chain MA [auth A] SDF format, chain KB [auth G] SDF format, chain IA [auth M] SDF format, chain GB [auth F] SDF format, chain EA [auth L] SDF format, chain CB [auth E] SDF format, chain AC [auth P] SDF format, chain AA [auth K] MOL2 format, chain YA [auth N] MOL2 format, chain WB [auth O] MOL2 format, chain W [auth J] MOL2 format, chain UA [auth D] MOL2 format, chain SB [auth I] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain OB [auth H] MOL2 format, chain MA [auth A] MOL2 format, chain KB [auth G] MOL2 format, chain IA [auth M] MOL2 format, chain GB [auth F] MOL2 format, chain EA [auth L] MOL2 format, chain CB [auth E] MOL2 format, chain AC [auth P] MOL2 format, chain AA [auth K] mmCIF format, chain YA [auth N] mmCIF format, chain WB [auth O] mmCIF format, chain W [auth J] mmCIF format, chain UA [auth D] mmCIF format, chain SB [auth I] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain OB [auth H] mmCIF format, chain MA [auth A] mmCIF format, chain KB [auth G] mmCIF format, chain IA [auth M] mmCIF format, chain GB [auth F] mmCIF format, chain EA [auth L] mmCIF format, chain CB [auth E] mmCIF format, chain AC [auth P] mmCIF format, chain AA [auth K]	AA [auth K] AC [auth P] CB [auth E] EA [auth L] GB [auth F] AA [auth K], AC [auth P], CB [auth E], EA [auth L], GB [auth F], IA [auth M], KB [auth G], MA [auth A], OB [auth H], QA [auth C], S [auth B], SB [auth I], UA [auth D], W [auth J], WB [auth O], YA [auth N]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain AA [auth K] Focus chain AC [auth P] Focus chain CB [auth E] Focus chain EA [auth L] Focus chain GB [auth F] Focus chain IA [auth M] Focus chain KB [auth G] Focus chain MA [auth A] Focus chain OB [auth H] Focus chain QA [auth C] Focus chain S [auth B] Focus chain SB [auth I] Focus chain UA [auth D] Focus chain W [auth J] Focus chain WB [auth O] Focus chain YA [auth N] Interactions & Density Focus chain AA [auth K] Focus chain AC [auth P] Focus chain CB [auth E] Focus chain EA [auth L] Focus chain GB [auth F] Focus chain IA [auth M] Focus chain KB [auth G] Focus chain MA [auth A] Focus chain OB [auth H] Focus chain QA [auth C] Focus chain S [auth B] Focus chain SB [auth I] Focus chain UA [auth D] Focus chain W [auth J] Focus chain WB [auth O] Focus chain YA [auth N]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain ZA [auth N] SDF format, chain XB [auth O] SDF format, chain X [auth J] SDF format, chain VA [auth D] SDF format, chain TB [auth I] SDF format, chain T [auth B] SDF format, chain RA [auth C] SDF format, chain PB [auth H] SDF format, chain NA [auth A] SDF format, chain LB [auth G] SDF format, chain JA [auth M] SDF format, chain HB [auth F] SDF format, chain FA [auth L] SDF format, chain DB [auth E] SDF format, chain BC [auth P] SDF format, chain BA [auth K] MOL2 format, chain ZA [auth N] MOL2 format, chain XB [auth O] MOL2 format, chain X [auth J] MOL2 format, chain VA [auth D] MOL2 format, chain TB [auth I] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain PB [auth H] MOL2 format, chain NA [auth A] MOL2 format, chain LB [auth G] MOL2 format, chain JA [auth M] MOL2 format, chain HB [auth F] MOL2 format, chain FA [auth L] MOL2 format, chain DB [auth E] MOL2 format, chain BC [auth P] MOL2 format, chain BA [auth K] mmCIF format, chain ZA [auth N] mmCIF format, chain XB [auth O] mmCIF format, chain X [auth J] mmCIF format, chain VA [auth D] mmCIF format, chain TB [auth I] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain PB [auth H] mmCIF format, chain NA [auth A] mmCIF format, chain LB [auth G] mmCIF format, chain JA [auth M] mmCIF format, chain HB [auth F] mmCIF format, chain FA [auth L] mmCIF format, chain DB [auth E] mmCIF format, chain BC [auth P] mmCIF format, chain BA [auth K]	BA [auth K] BC [auth P] DB [auth E] FA [auth L] HB [auth F] BA [auth K], BC [auth P], DB [auth E], FA [auth L], HB [auth F], JA [auth M], LB [auth G], NA [auth A], PB [auth H], RA [auth C], T [auth B], TB [auth I], VA [auth D], X [auth J], XB [auth O], ZA [auth N]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth K] Focus chain BC [auth P] Focus chain DB [auth E] Focus chain FA [auth L] Focus chain HB [auth F] Focus chain JA [auth M] Focus chain LB [auth G] Focus chain NA [auth A] Focus chain PB [auth H] Focus chain RA [auth C] Focus chain T [auth B] Focus chain TB [auth I] Focus chain VA [auth D] Focus chain X [auth J] Focus chain XB [auth O] Focus chain ZA [auth N] Interactions & Density Focus chain BA [auth K] Focus chain BC [auth P] Focus chain DB [auth E] Focus chain FA [auth L] Focus chain HB [auth F] Focus chain JA [auth M] Focus chain LB [auth G] Focus chain NA [auth A] Focus chain PB [auth H] Focus chain RA [auth C] Focus chain T [auth B] Focus chain TB [auth I] Focus chain VA [auth D] Focus chain X [auth J] Focus chain XB [auth O] Focus chain ZA [auth N]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain YB [auth P] SDF format, chain Y [auth K] SDF format, chain WA [auth N] SDF format, chain UB [auth O] SDF format, chain U [auth J] SDF format, chain SA [auth D] SDF format, chain QB [auth I] SDF format, chain Q [auth B] SDF format, chain OA [auth C] SDF format, chain MB [auth H] SDF format, chain KA [auth A] SDF format, chain IB [auth G] SDF format, chain GA [auth M] SDF format, chain EB [auth F] SDF format, chain CA [auth L] SDF format, chain AB [auth E] MOL2 format, chain YB [auth P] MOL2 format, chain Y [auth K] MOL2 format, chain WA [auth N] MOL2 format, chain UB [auth O] MOL2 format, chain U [auth J] MOL2 format, chain SA [auth D] MOL2 format, chain QB [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain MB [auth H] MOL2 format, chain KA [auth A] MOL2 format, chain IB [auth G] MOL2 format, chain GA [auth M] MOL2 format, chain EB [auth F] MOL2 format, chain CA [auth L] MOL2 format, chain AB [auth E] mmCIF format, chain YB [auth P] mmCIF format, chain Y [auth K] mmCIF format, chain WA [auth N] mmCIF format, chain UB [auth O] mmCIF format, chain U [auth J] mmCIF format, chain SA [auth D] mmCIF format, chain QB [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain MB [auth H] mmCIF format, chain KA [auth A] mmCIF format, chain IB [auth G] mmCIF format, chain GA [auth M] mmCIF format, chain EB [auth F] mmCIF format, chain CA [auth L] mmCIF format, chain AB [auth E]	AB [auth E] CA [auth L] EB [auth F] GA [auth M] IB [auth G] AB [auth E], CA [auth L], EB [auth F], GA [auth M], IB [auth G], KA [auth A], MB [auth H], OA [auth C], Q [auth B], QB [auth I], SA [auth D], U [auth J], UB [auth O], WA [auth N], Y [auth K], YB [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain CA [auth L] Focus chain EB [auth F] Focus chain GA [auth M] Focus chain IB [auth G] Focus chain KA [auth A] Focus chain MB [auth H] Focus chain OA [auth C] Focus chain Q [auth B] Focus chain QB [auth I] Focus chain SA [auth D] Focus chain U [auth J] Focus chain UB [auth O] Focus chain WA [auth N] Focus chain Y [auth K] Focus chain YB [auth P] Interactions & Density Focus chain AB [auth E] Focus chain CA [auth L] Focus chain EB [auth F] Focus chain GA [auth M] Focus chain IB [auth G] Focus chain KA [auth A] Focus chain MB [auth H] Focus chain OA [auth C] Focus chain Q [auth B] Focus chain QB [auth I] Focus chain SA [auth D] Focus chain U [auth J] Focus chain UB [auth O] Focus chain WA [auth N] Focus chain Y [auth K] Focus chain YB [auth P]