7CGP | pdb_00007cgp

Cryo-EM structure of the human mitochondrial translocase TIM22 complex at 3.7 angstrom.

PDB DOI: https://doi.org/10.2210/pdb7CGP/pdb
EM Map EMD-9958: EMDB EMDataResource

Classification: TRANSLOCASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMmpstruc

Deposited: 2020-07-01 Released: 2020-10-14
Deposition Author(s): Qi, L., Wang, Q., Guan, Z., Yan, C., Yin, P.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Cryo-EM structure of the human mitochondrial translocase TIM22 complex.

Qi, L., Wang, Q., Guan, Z., Wu, Y., Shen, C., Hong, S., Cao, J., Zhang, X., Yan, C., Yin, P.

(2021) Cell Res 31: 369-372

PubMed: 32901109 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-020-00400-w
Primary Citation of Related Structures:
7CGP

Organizational Affiliation

National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.

Macromolecule Content

Total Structure Weight: 222.92 kDa
Atom Count: 12,433
Modeled Residue Count: 1,569
Deposited Residue Count: 1,964
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import inner membrane translocase subunit Tim22	A	194	Homo sapiens	Mutation(s): 0 Gene Names: TIMM22, TEX4, TIM22 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y584 (Homo sapiens) Explore Q9Y584 Go to UniProtKB: Q9Y584
PHAROS: Q9Y584 GTEx: ENSG00000177370
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y584
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylglycerol kinase, mitochondrial	B	422	Homo sapiens	Mutation(s): 0 Gene Names: AGK, MULK EC: 2.7.1.107 (PDB Primary Data), 2.7.1.138 (PDB Primary Data), 2.7.1.94 (PDB Primary Data) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q53H12 (Homo sapiens) Explore Q53H12 Go to UniProtKB: Q53H12
PHAROS: Q53H12 GTEx: ENSG00000006530
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q53H12
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import inner membrane translocase subunit Tim29	C	260	Homo sapiens	Mutation(s): 0 Gene Names: TIMM29, c19orf52 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSF4 (Homo sapiens) Explore Q9BSF4 Go to UniProtKB: Q9BSF4
PHAROS: Q9BSF4 GTEx: ENSG00000142444
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BSF4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import inner membrane translocase subunit Tim9	D, E, F, K, L	89	Homo sapiens	Mutation(s): 0 Gene Names: TIMM9, TIM9, TIM9A, TIMM9A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5J7 (Homo sapiens) Explore Q9Y5J7 Go to UniProtKB: Q9Y5J7
PHAROS: Q9Y5J7 GTEx: ENSG00000100575
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5J7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import inner membrane translocase subunit Tim10	G, H, I, M, N G, H, I, M, N, O	90	Homo sapiens	Mutation(s): 0 Gene Names: TIMM10, TIM10 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P62072 (Homo sapiens) Explore P62072 Go to UniProtKB: P62072
PHAROS: P62072 GTEx: ENSG00000134809
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62072
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import inner membrane translocase subunit Tim10 B	J	103	Homo sapiens	Mutation(s): 0 Gene Names: TIMM10B, FXC1, TIM9B, TIMM9B Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5J6 (Homo sapiens) Explore Q9Y5J6 Go to UniProtKB: Q9Y5J6
PHAROS: Q9Y5J6 GTEx: ENSG00000132286
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5J6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEE (Subject of Investigation/LOI) Query on PEE Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFA0507700
National Natural Science Foundation of China (NSFC)	China	31722017

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2021-03-17
Changes: Database references
Version 2.0: 2025-04-09
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2025-06-18
Changes: Data collection