9J99 | pdb_00009j99

Substrate-engaged TOM complex from yeast


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dynamic TOM-TIM23 supercomplex directs mitochondrial protein translocation and sorting.

Yang, Y.Wang, S.Wang, G.Lian, Y.Xue, L.Jiang, W.Guo, Q.Song, C.Li, L.

(2025) Nat Struct Mol Biol 32: 2231-2241

  • DOI: https://doi.org/10.1038/s41594-025-01662-x
  • Primary Citation Related Structures: 
    9J99, 9J9B

  • PubMed Abstract: 

    The mitochondrial translocase of the outer membrane (TOM) and translocase of the inner membrane 23 (TIM23) complexes are coupled to control protein import across the outer and inner membranes, respectively. However, the mechanisms of protein recognition and sorting in the TOM-TIM23 pathway remain unclear. Here we report cryo-electron microscopy structures of a translocating polypeptide substrate captured in the active TOM-TIM23 supercomplex from Saccharomyces cerevisiae. In the TOM complex, the polypeptide substrate adopts multiple conformations stabilized by hydrophilic residues from distinct regions of the Tom40 channel. In the TIM23 complex, the Tim17 and Mgr2 subunits create the translocation pathway, with a central restriction formed by four highly conserved hydrophobic residues. The substrate primarily interacts with hydrophobic residues along the Tim17-Mgr2 pathway. Substrate hydrophobicity modulates the association of Mgr2 with Tim17, enabling dynamic regulation of protein sorting toward either the matrix or membrane. These findings reveal a sophisticated translocation mechanism of the TOM-TIM23 supercomplex that ensures the efficient import of diverse mitochondrial proteins.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM40A,
F [auth I]
387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM40ISP42MOM38YMR203WYM8325.04
Membrane Entity: Yes 
UniProt
Find proteins for P23644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P23644
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23644
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM22B,
G [auth J]
152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM22MAS17MAS22MOM22YNL131WN1217N1862
Membrane Entity: Yes 
UniProt
Find proteins for P49334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P49334
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UniProt GroupP49334
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM5C,
H [auth K]
50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM5MOM8AYPR133W-A
Membrane Entity: Yes 
UniProt
Find proteins for P80967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP80967
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM6D,
I [auth L]
61Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM6ISP6YOR045W
Membrane Entity: Yes 
UniProt
Find proteins for P33448 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP33448
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM7E,
J [auth M]
60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOM7MOM7YNL070WN2378
Membrane Entity: Yes 
UniProt
Find proteins for P53507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53507 
Go to UniProtKB:  P53507
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UniProt GroupP53507
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download Ideal Coordinates CCD File 
AB [auth L]
CA [auth D]
DA [auth D]
EA [auth D]
FB [auth M]
AB [auth L],
CA [auth D],
DA [auth D],
EA [auth D],
FB [auth M],
JA [auth E],
L [auth A],
LA [auth I],
M [auth A],
MA [auth I],
N [auth A],
NA [auth I],
O [auth A],
PA [auth I],
QA [auth I],
S [auth A],
SA [auth I],
TA [auth I],
U [auth A],
UA [auth I],
V [auth A],
X [auth B],
Y [auth B],
YA [auth J],
ZA [auth J]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
UND (Subject of Investigation/LOI)
Query on UND

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth D]
BB [auth L]
CB [auth L]
DB [auth L]
AA [auth C],
BA [auth D],
BB [auth L],
CB [auth L],
DB [auth L],
EB [auth M],
FA [auth D],
GA [auth D],
GB [auth M],
HA [auth E],
HB [auth M],
IA [auth E],
IB [auth M],
K [auth A],
KA [auth E],
OA [auth I],
P [auth A],
Q [auth A],
R [auth A],
RA [auth I],
T [auth A],
VA [auth I],
W [auth B],
WA [auth I],
XA [auth I],
Z [auth C]
UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271269

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Data collection, Database references