9I6B | pdb_00009i6b

CryoEM structure of the Chaetomium thermophilum TOM core complex at 2.7 angstrom resolution (pALDH treated)

PDB DOI: https://doi.org/10.2210/pdb9I6B/pdb
EM Map EMD-52652: EMDB EMDataResource

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

Deposited: 2025-01-29 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: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

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

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

Literature

Structures of Chaetomium thermophilum TOM complexes with bound preproteins.

Agip, A.A., Ornelas, P., Yang, T.J., Uboldi, E., Hader, S., McDowell, M.A., Kuhlbrandt, W.

(2025) Proc Natl Acad Sci U S A 122: e2507279122-e2507279122

PubMed: 40674418 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.2507279122
Primary Citation of Related Structures:
9I6B, 9I7P, 9I7S, 9I7T

PubMed Abstract:
Mitochondria import most of their proteins from the cytoplasm through the TOM complex. Preproteins containing targeting signals are recognized by the TOM receptor subunits and translocated by Tom40 across the outer mitochondrial membrane. We present four structures of the preprotein-bound and preprotein-free TOM core and holo complexes from the thermophilic fungus Chaetomium thermophilum , obtained by single-particle electron cryomicroscopy. Our structures reveal the symmetric arrangement of two copies of the Tom20 receptor subunit in the TOM holo complex. Several different conformations of Tom20 within the TOM holo complex highlight the dynamic nature of the receptor. The structure of preprotein-bound Tom20 provides insight into the early stages of protein translocation.

Organizational Affiliation

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt 60438, Germany.

Macromolecule Content

Total Structure Weight: 171.76 kDa
Atom Count: 8,644
Modeled Residue Count: 1,020
Deposited Residue Count: 1,454
Unique protein chains: 5

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], F [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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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit tom5	B [auth E], G [auth F]	50	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
UniProt
Find proteins for A0AAJ0H4I1 (Chaetomium strumarium) Explore A0AAJ0H4I1 Go to UniProtKB: A0AAJ0H4I1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAJ0H4I1
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], 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
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Import receptor subunit-like protein	D [auth I], I [auth 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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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit (Tom40)-like protein	E [auth A], J [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 CA [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth I] SDF format, chain O [auth A] SDF format, chain S [auth A] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth J] SDF format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth I] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth J] MOL2 format, chain Z [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth I] mmCIF format, chain O [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth J] mmCIF format, chain Z [auth B]	CA [auth B] K [auth C] L [auth C] N [auth I] O [auth A] CA [auth B], K [auth C], L [auth C], N [auth I], O [auth A], S [auth A], U [auth D], V [auth D], X [auth J], Z [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain CA [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth I] Focus chain O [auth A] Focus chain S [auth A] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth J] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth I] Focus chain O [auth A] Focus chain S [auth A] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth J] Focus chain Z [auth B]
PLC Query on PLC Download Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
DU0 Query on DU0 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain M [auth G] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth A] SDF format, chain W [auth H] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain M [auth G] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth H] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain M [auth G] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth A] mmCIF format, chain W [auth H] mmCIF format, chain Y [auth B]	AA [auth B] BA [auth B] M [auth G] P [auth A] Q [auth A] AA [auth B], BA [auth B], M [auth G], P [auth A], Q [auth A], T [auth A], W [auth H], Y [auth B]	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 B] Focus chain BA [auth B] Focus chain M [auth G] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth A] Focus chain W [auth H] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain M [auth G] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth A] Focus chain W [auth H] Focus chain Y [auth B]