6UCU

Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution.

Tucker, K.Park, E.

(2019) Nat Struct Mol Biol 26: 1158-1166

  • DOI: https://doi.org/10.1038/s41594-019-0339-2
  • Primary Citation of Related Structures:  
    6UCU, 6UCV

  • PubMed Abstract: 

    Nearly all mitochondrial proteins are encoded by the nuclear genome and imported into mitochondria after synthesis on cytosolic ribosomes. These precursor proteins are translocated into mitochondria by the TOM complex, a protein-conducting channel in the mitochondrial outer membrane. We have determined high-resolution cryo-EM structures of the core TOM complex from Saccharomyces cerevisiae in dimeric and tetrameric forms. Dimeric TOM consists of two copies each of five proteins arranged in two-fold symmetry: pore-forming β-barrel protein Tom40 and four auxiliary α-helical transmembrane proteins. The pore of each Tom40 has an overall negatively charged inner surface attributed to multiple functionally important acidic patches. The tetrameric complex is essentially a dimer of dimeric TOM, which may be capable of forming higher-order oligomers. Our study reveals the detailed molecular organization of the TOM complex and provides new insights about the mechanism of protein translocation into mitochondria.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM40A,
F [auth I]
397Saccharomyces 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
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UniProt GroupP23644
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM22B,
G [auth J]
162Saccharomyces 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))
Explore P33448 
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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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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth I]
BA [auth B]
BB [auth I]
CA [auth B]
AA [auth A],
AB [auth I],
BA [auth B],
BB [auth I],
CA [auth B],
CB [auth I],
DA [auth B],
DB [auth I],
EA [auth B],
EB [auth I],
FA [auth C],
FB [auth J],
GA [auth C],
GB [auth J],
HA [auth D],
HB [auth J],
IA [auth D],
IB [auth J],
JA [auth D],
JB [auth K],
K [auth A],
KA [auth E],
KB [auth K],
L [auth A],
LA [auth E],
LB [auth L],
M [auth A],
MA [auth E],
MB [auth L],
N [auth A],
NA [auth E],
NB [auth L],
O [auth A],
OA [auth I],
OB [auth M],
P [auth A],
PA [auth I],
PB [auth M],
Q [auth A],
QA [auth I],
QB [auth M],
R [auth A],
RA [auth I],
RB [auth M],
S [auth A],
SA [auth I],
T [auth A],
TA [auth I],
U [auth A],
UA [auth I],
V [auth A],
VA [auth I],
W [auth A],
WA [auth I],
X [auth A],
XA [auth I],
Y [auth A],
YA [auth I],
Z [auth A],
ZA [auth I]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.8.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-1752814
The Vallee FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Database references
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references