5XTB

Cryo-EM structure of human respiratory complex I matrix arm

  • Classification: OXIDOREDUCTASE/ELECTRON TRANSPORT
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2017-06-18 Released: 2017-08-30 
  • Deposition Author(s): Gu, J., Wu, M., Yang, M.
  • Funding Organization(s): Ministry of Science and Technology, National Science Fund for Distinguished Young Scholars, National Natural Science Foundation of China

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:  
    5XTI, 5XTB, 5XTD, 5XTC, 5XTE, 5XTH

  • 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 megacomple ...

    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
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialA431Homo sapiensMutation(s): 0 
Gene Names: NDUFV1UQOR1
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for P49821 (Homo sapiens)
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PHAROS  P49821
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialB176Homo sapiensMutation(s): 0 
Gene Names: NDUFS8
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for O00217 (Homo sapiens)
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PHAROS  O00217
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialC156Homo sapiensMutation(s): 0 
Gene Names: NDUFS7
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for O75251 (Homo sapiens)
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PHAROS  O75251
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6E113Homo sapiensMutation(s): 0 
Gene Names: NDUFA6LYRM6NADHB14
Find proteins for P56556 (Homo sapiens)
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PHAROS  P56556
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2F83Homo sapiensMutation(s): 0 
Gene Names: NDUFA2
Find proteins for O43678 (Homo sapiens)
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PHAROS  O43678
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialG85Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
Find proteins for O14561 (Homo sapiens)
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PHAROS  O14561
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5H112Homo sapiensMutation(s): 0 
Gene Names: NDUFA5
Find proteins for Q16718 (Homo sapiens)
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PHAROS  Q16718
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7I110Homo sapiensMutation(s): 0 
Gene Names: NDUFA7
Find proteins for O95182 (Homo sapiens)
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PHAROS  O95182
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialJ337Homo sapiensMutation(s): 0 
Gene Names: NDUFA9NDUFS2L
Find proteins for Q16795 (Homo sapiens)
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PHAROS  Q16795
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialK33Homo sapiensMutation(s): 0 
Gene Names: NDUFV3
Find proteins for P56181 (Homo sapiens)
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PHAROS  P56181
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialL118Homo sapiensMutation(s): 0 
Gene Names: NDUFS4
Find proteins for O43181 (Homo sapiens)
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PHAROS  O43181
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialM687Homo sapiensMutation(s): 0 
Gene Names: NDUFS1
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for P28331 (Homo sapiens)
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PHAROS  P28331
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12N143Homo sapiensMutation(s): 0 
Gene Names: NDUFA12DAP13
Find proteins for Q9UI09 (Homo sapiens)
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PHAROS  Q9UI09
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialO212Homo sapiensMutation(s): 0 
Gene Names: NDUFV2
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for P19404 (Homo sapiens)
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PHAROS  P19404
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialP208Homo sapiensMutation(s): 0 
Gene Names: NDUFS3
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for O75489 (Homo sapiens)
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PHAROS  O75489
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialQ385Homo sapiensMutation(s): 0 
Gene Names: NDUFS2
EC: 1.6.5.3 (PDB Primary Data), 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
Find proteins for O75306 (Homo sapiens)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialT95Homo sapiensMutation(s): 0 
Gene Names: NDUFS6
Find proteins for O75380 (Homo sapiens)
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PHAROS  O75380
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13W22Homo sapiensMutation(s): 0 
Gene Names: NDUFA13GRIM19CDA016CGI-39
Find proteins for Q9P0J0 (Homo sapiens)
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PHAROS  Q9P0J0
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

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J
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
8Q1
Query on 8Q1

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E
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
 Ligand Interaction
FMN
Query on FMN

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A
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

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A, B, C, M
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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M, O
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

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-06-18 
  • Released Date: 2017-08-30 
  • Deposition Author(s): Gu, J., Wu, M., Yang, M.

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

Revision History 

  • 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: Advisory, Derived calculations