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: 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 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. Electronic address: maojunyang@tsinghua.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8A, L [auth N]81Homo sapiensMutation(s): 0 
Gene Names: UQCRQ
Membrane Entity: Yes 
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Find proteins for O14949 (Homo sapiens)
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PHAROS:  O14949
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialB, M [auth O]57Homo sapiensMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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PHAROS:  P47985
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialC, N [auth P]196Homo sapiensMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9D, O [auth Q]62Homo sapiensMutation(s): 0 
Gene Names: UQCR10UCRCHSPC119
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialE, P [auth R]75Homo sapiensMutation(s): 0 
Gene Names: UQCRH
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F, Q [auth S]106Homo sapiensMutation(s): 0 
Gene Names: UQCRBUQBP
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10G, R [auth T]51Homo sapiensMutation(s): 0 
Gene Names: UQCR11UQCR
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialH, S [auth U]241Homo sapiensMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bI [auth J], T [auth V]378Homo sapiensMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialJ [auth K], U [auth W]419Homo sapiensMutation(s): 0 
Gene Names: UQCRC2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialK [auth L], V [auth Y]446Homo sapiensMutation(s): 0 
Gene Names: UQCRC1
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BA [auth H] , FA [auth J] , GA [auth J] , IA [auth L] , KA [auth N] , QA [auth U] , UA [auth Y] , W [auth A] , 
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
 Ligand Interaction
PLX (Subject of Investigation/LOI)
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
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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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
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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AA [auth H], PA [auth U]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
CA [auth J], DA [auth J], RA [auth V], SA [auth V]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FES
Query on FES

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-06-19 
  • Released Date: 2017-08-30 
  • Deposition Author(s): Gu, J., Wu, M., Yang, M.

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