9EII | pdb_00009eii

Import stalled PINK1 TOM complex, symmetry expanded

PDB DOI: https://doi.org/10.2210/pdb9EII/pdb
EM Map EMD-48084: EMDB EMDataResource

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

Deposited: 2024-11-26 Released: 2025-03-12
Deposition Author(s): Kirk, N.S., Glukhova, A.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.75 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of human PINK1 at a mitochondrial TOM-VDAC array

Callegari, S., Kirk, N.S., Gan, Z.Y., Cobbold, S.A., Dite, T., Leis, A., Dagley, L.F., Glukhova, A., Komander, D.

(2025) Science

DOI: https://doi.org/10.1126/science.adu6445

Macromolecule Content

Total Structure Weight: 268.13 kDa
Atom Count: 14,448
Modelled Residue Count: 1,789
Deposited Residue Count: 2,408
Unique protein chains: 8

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PINK1, mitochondrial	A [auth B]	603	Homo sapiens	Mutation(s): 0 Gene Names: PINK1 EC: 2.7.11.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXM7 (Homo sapiens) Explore Q9BXM7 Go to UniProtKB: Q9BXM7
PHAROS: Q9BXM7 GTEx: ENSG00000158828
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BXM7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM20 homolog	B [auth D]	145	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q15388 (Homo sapiens) Explore Q15388 Go to UniProtKB: Q15388
PHAROS: Q15388 GTEx: ENSG00000173726
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15388
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent anion-selective channel protein 2	C [auth F]	294	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P45880 (Homo sapiens) Explore P45880 Go to UniProtKB: P45880
PHAROS: P45880 GTEx: ENSG00000165637
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P45880
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM40 homolog	D [auth I], E [auth J]	361	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O96008 (Homo sapiens) Explore O96008 Go to UniProtKB: O96008
PHAROS: O96008 GTEx: ENSG00000130204
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O96008
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM5 homolog	F [auth L], M [auth Z]	51	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4H5 (Homo sapiens) Explore Q8N4H5 Go to UniProtKB: Q8N4H5
GTEx: ENSG00000175768
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N4H5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM7 homolog	G [auth N], L [auth X]	55	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0U1 (Homo sapiens) Explore Q9P0U1 Go to UniProtKB: Q9P0U1
PHAROS: Q9P0U1 GTEx: ENSG00000196683
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9P0U1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM6 homolog	H [auth P], K [auth V]	74	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96B49 (Homo sapiens) Explore Q96B49 Go to UniProtKB: Q96B49
PHAROS: Q96B49 GTEx: ENSG00000214736
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96B49
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM22 homolog	I [auth R], J [auth T]	142	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NS69 (Homo sapiens) Explore Q9NS69 Go to UniProtKB: Q9NS69
PHAROS: Q9NS69 GTEx: ENSG00000100216
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NS69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain O [auth I] SDF format, chain P [auth I] SDF format, chain Q [auth I] SDF format, chain S [auth N] SDF format, chain T [auth N] SDF format, chain U [auth R] SDF format, chain V [auth T] SDF format, chain R [auth J] MOL2 format, chain N [auth F] MOL2 format, chain O [auth I] MOL2 format, chain P [auth I] MOL2 format, chain Q [auth I] MOL2 format, chain S [auth N] MOL2 format, chain T [auth N] MOL2 format, chain U [auth R] MOL2 format, chain V [auth T] MOL2 format, chain R [auth J] mmCIF format, chain N [auth F] mmCIF format, chain O [auth I] mmCIF format, chain P [auth I] mmCIF format, chain Q [auth I] mmCIF format, chain S [auth N] mmCIF format, chain T [auth N] mmCIF format, chain U [auth R] mmCIF format, chain V [auth T] mmCIF format, chain R [auth J]	N [auth F] O [auth I] P [auth I] Q [auth I] R [auth J] N [auth F], O [auth I], P [auth I], Q [auth I], R [auth J], S [auth N], T [auth N], U [auth R], V [auth T]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain N [auth F] Focus chain O [auth I] Focus chain P [auth I] Focus chain Q [auth I] Focus chain R [auth J] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth R] Focus chain V [auth T] Interactions & Density Focus chain N [auth F] Focus chain O [auth I] Focus chain P [auth I] Focus chain Q [auth I] Focus chain R [auth J] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth R] Focus chain V [auth T]