9I7S | pdb_00009i7s

CryoEM structure of the Chaetomium thermophilum TOM holo complex at 3.2 angstrom resolution (pALDH treated)

PDB DOI: https://doi.org/10.2210/pdb9I7S/pdb
EM Map EMD-52660: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Thermochaetoides thermophila DSM 1495
Mutation(s): No

Deposited: 2025-02-01 Released: 2025-07-09
Deposition Author(s): Agip, A.N.A., Ornelas, P., Yang, T.J., Ermanno, U., Haeder, S., McDowell, M.A., Kuehlbrandt, W.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

CryoEM structure of the Chaetomium thermophilum TOM holo complex at 3.2 angstrom (pALDH treated)

Agip, A.N.A., Ornelas, P., Yang, T.J., Ermanno, U., Haeder, S., McDowell, M.A., Kuehlbrandt, W.

To be published.

Macromolecule Content

Total Structure Weight: 212.22 kDa
Atom Count: 11,338
Modeled Residue Count: 1,358
Deposited Residue Count: 1,824
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 receptor subunit tom22	A [auth C], G [auth D]	175	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0026640
UniProt
Find proteins for G0S6L5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S6L5 Go to UniProtKB: G0S6L5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0S6L5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit Tom5	B [auth E], H [auth F]	50	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit tom6	C [auth G], I [auth H]	84	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
UniProt
Find proteins for G0S9G0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S9G0 Go to UniProtKB: G0S9G0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0S9G0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Import receptor subunit-like protein	D [auth I], J	71	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
UniProt
Find proteins for G0SE07 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SE07 Go to UniProtKB: G0SE07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0SE07
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tom20	E [auth K], K [auth L]	185	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
UniProt
Find proteins for G0S6E4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S6E4 Go to UniProtKB: G0S6E4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0S6E4
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 receptor subunit (Tom40)-like protein	F [auth A], L [auth B]	347	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
UniProt
Find proteins for G0S7S2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S7S2 Go to UniProtKB: G0S7S2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0S7S2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth A] SDF format, chain V [auth A] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain BA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain BA [auth B]	BA [auth B] EA [auth B] M [auth C] O [auth C] P [auth C] BA [auth B], EA [auth B], M [auth C], O [auth C], P [auth C], R [auth A], V [auth A], W [auth D], X [auth D], Y [auth D]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain BA [auth B] Focus chain EA [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth A] Focus chain V [auth A] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth B] Focus chain EA [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth A] Focus chain V [auth A] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
PLC Query on PLC Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
DU0 Query on DU0 Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth G] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Z [auth D] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth G] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth G] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Z [auth D]	AA [auth H] CA [auth B] DA [auth B] N [auth C] Q [auth G] AA [auth H], CA [auth B], DA [auth B], N [auth C], Q [auth G], S [auth A], T [auth A], Z [auth D]	2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol C₃₂ H₅₂ O₅ GFDJQXOBWHMOSQ-LEZUHYJESA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain N [auth C] Focus chain Q [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain N [auth C] Focus chain Q [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth D]