5XTB

Cryo-EM structure of human respiratory complex I matrix arm

  • Classification: OXIDOREDUCTASE/ELECTRON TRANSPORT
  • Organism(s): Homo sapiens

  • 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: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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.,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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
A
431Homo sapiensMutation(s): 0 
Gene Names: NDUFV1 (UQOR1)
EC: 1.6.99.3, 7.1.1.2
Find proteins for P49821 (Homo sapiens)
Go to Gene View: NDUFV1
Go to UniProtKB:  P49821
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
B
176Homo sapiensMutation(s): 0 
Gene Names: NDUFS8
EC: 1.6.99.3, 7.1.1.2
Find proteins for O00217 (Homo sapiens)
Go to Gene View: NDUFS8
Go to UniProtKB:  O00217
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
C
156Homo sapiensMutation(s): 0 
Gene Names: NDUFS7
EC: 1.6.99.3, 7.1.1.2
Find proteins for O75251 (Homo sapiens)
Go to Gene View: NDUFS7
Go to UniProtKB:  O75251
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
E
113Homo sapiensMutation(s): 0 
Gene Names: NDUFA6 (LYRM6, NADHB14)
Find proteins for P56556 (Homo sapiens)
Go to Gene View: NDUFA6
Go to UniProtKB:  P56556
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
F
83Homo sapiensMutation(s): 0 
Gene Names: NDUFA2
Find proteins for O43678 (Homo sapiens)
Go to Gene View: NDUFA2
Go to UniProtKB:  O43678
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein, mitochondrial
G
85Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
Find proteins for O14561 (Homo sapiens)
Go to Gene View: NDUFAB1
Go to UniProtKB:  O14561
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
H
112Homo sapiensMutation(s): 0 
Gene Names: NDUFA5
Find proteins for Q16718 (Homo sapiens)
Go to Gene View: NDUFA5
Go to UniProtKB:  Q16718
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
I
110Homo sapiensMutation(s): 0 
Gene Names: NDUFA7
Find proteins for O95182 (Homo sapiens)
Go to Gene View: NDUFA7
Go to UniProtKB:  O95182
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
J
337Homo sapiensMutation(s): 0 
Gene Names: NDUFA9 (NDUFS2L)
Find proteins for Q16795 (Homo sapiens)
Go to Gene View: NDUFA9
Go to UniProtKB:  Q16795
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
K
33Homo sapiensMutation(s): 0 
Gene Names: NDUFV3
Find proteins for P56181 (Homo sapiens)
Go to Gene View: NDUFV3
Go to UniProtKB:  P56181
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
L
118Homo sapiensMutation(s): 0 
Gene Names: NDUFS4
Find proteins for O43181 (Homo sapiens)
Go to Gene View: NDUFS4
Go to UniProtKB:  O43181
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
M
687Homo sapiensMutation(s): 0 
Gene Names: NDUFS1
EC: 1.6.99.3, 7.1.1.2
Find proteins for P28331 (Homo sapiens)
Go to Gene View: NDUFS1
Go to UniProtKB:  P28331
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
N
143Homo sapiensMutation(s): 0 
Gene Names: NDUFA12 (DAP13)
Find proteins for Q9UI09 (Homo sapiens)
Go to Gene View: NDUFA12
Go to UniProtKB:  Q9UI09
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
O
212Homo sapiensMutation(s): 0 
Gene Names: NDUFV2
EC: 1.6.99.3, 7.1.1.2
Find proteins for P19404 (Homo sapiens)
Go to Gene View: NDUFV2
Go to UniProtKB:  P19404
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
P
208Homo sapiensMutation(s): 0 
Gene Names: NDUFS3
EC: 1.6.99.3, 7.1.1.2
Find proteins for O75489 (Homo sapiens)
Go to Gene View: NDUFS3
Go to UniProtKB:  O75489
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
Q
385Homo sapiensMutation(s): 0 
Gene Names: NDUFS2
EC: 1.6.99.3, 7.1.1.2
Find proteins for O75306 (Homo sapiens)
Go to Gene View: NDUFS2
Go to UniProtKB:  O75306
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
T
95Homo sapiensMutation(s): 0 
Gene Names: NDUFS6
Find proteins for O75380 (Homo sapiens)
Go to Gene View: NDUFS6
Go to UniProtKB:  O75380
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
W
22Homo sapiensMutation(s): 0 
Gene Names: NDUFA13 (GRIM19)
Find proteins for Q9P0J0 (Homo sapiens)
Go to Gene View: NDUFA13
Go to UniProtKB:  Q9P0J0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C, M
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
M, O
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
8Q1
Query on 8Q1

Download SDF File 
Download CCD File 
E
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
S-dodecanoyl-4'-phosphopantetheine
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
J
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2017-12-06
    Type: Data processing, Database references