5XTE

Cryo-EM structure of human respiratory complex III (cytochrome bc1 complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.

Guo, R.Zong, S.Wu, M.Gu, J.Yang, M.

(2017) Cell 170: 1247-1257.e12

  • DOI: https://doi.org/10.1016/j.cell.2017.07.050
  • Primary Citation of Related Structures:  
    5XTB, 5XTC, 5XTD, 5XTE, 5XTH, 5XTI

  • PubMed Abstract: 

    The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-I 2 III 2 IV 2 (MCI 2 III 2 IV 2 ) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCI 2 III 2 IV 2 forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c 1 state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8A,
L [auth N]
81Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  O14949
GTEx:  ENSG00000164405 
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UniProt GroupO14949
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialB,
M [auth O]
57Homo sapiensMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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PHAROS:  P47985
GTEx:  ENSG00000169021 
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UniProt GroupP47985
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialC,
N [auth P]
196Homo sapiensMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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PHAROS:  P47985
GTEx:  ENSG00000169021 
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UniProt GroupP47985
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9D,
O [auth Q]
62Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  Q9UDW1
GTEx:  ENSG00000184076 
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UniProt GroupQ9UDW1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialE,
P [auth R]
75Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000173660 
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UniProt GroupP07919
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
Q [auth S]
106Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000156467 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10G,
R [auth T]
51Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000127540 
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UniProt GroupO14957
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialH,
S [auth U]
241Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000179091 
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UniProt GroupP08574
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bI [auth J],
T [auth V]
378Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000198727 
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UniProt GroupP00156
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialJ [auth K],
U [auth W]
419Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000140740 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialK [auth L],
V [auth Y]
446Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P31930
GTEx:  ENSG00000010256 
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UniProt GroupP31930
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BA [auth H]
FA [auth J]
GA [auth J]
IA [auth L]
KA [auth N]
BA [auth H],
FA [auth J],
GA [auth J],
IA [auth L],
KA [auth N],
QA [auth U],
UA [auth Y],
W [auth A],
Y [auth G]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PLX
Query on PLX

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HA [auth L],
MA [auth Q],
NA [auth T]
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
PEE
Query on PEE

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EA [auth J]
JA [auth L]
OA [auth U]
TA [auth V]
VA [auth Y]
EA [auth J],
JA [auth L],
OA [auth U],
TA [auth V],
VA [auth Y],
Z [auth H]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC
Query on HEC

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AA [auth H],
PA [auth U]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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CA [auth J],
DA [auth J],
RA [auth V],
SA [auth V]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES
Query on FES

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LA [auth P],
X [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.11.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21532004
National Natural Science Foundation of ChinaChina31570733
Ministry of Science and TechnologyChina2016YFA0501100
Ministry of Science and TechnologyChina2017YFA0504600
National Science Fund for Distinguished Young ScholarsChina31625008

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Data processing, Database references
  • Version 1.3: 2019-11-06
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.4: 2019-11-20
    Changes: Derived calculations