2YBB

Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19 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

Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I(1)III(2)Iv(1).

Althoff, T.Mills, D.J.Popot, J.-L.Kuehlbrandt, W.

(2011) Embo J. 30: 4652

  • DOI: 10.1038/emboj.2011.324

  • PubMed Abstract: 
  • The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized s ...

    The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized supercomplex I(1)III(2)IV(1) from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10-11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred.


    Related Citations: 
    • Strukturelle Untersuchungen Am Superkomplex I1III2Iv1 Der Atmungskette Mittels Kryoelektronenmikroskopie
      Althoff, T.
      (2011) Ph D Thesis --: --


    Organizational Affiliation

    Abteilung Strukturbiologie, Max-Planck-Institut für Biophysik, Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 1
1
438Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo1
EC: 1.6.5.11
Find proteins for Q56222 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56222
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 2
2
181Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo2
EC: 1.6.5.11
Find proteins for Q56221 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56221
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 3
3
783Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo3
EC: 1.6.5.11
Find proteins for Q56223 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56223
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 4
4
409Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo4
EC: 1.6.5.11
Find proteins for Q56220 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56220
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 5
5
207Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo5
EC: 1.6.5.11
Find proteins for Q56219 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56219
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 6
6
181Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo6
EC: 1.6.5.11
Find proteins for Q56218 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56218
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 15
7
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo15
EC: 1.6.5.11
Find proteins for Q5SKZ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKZ7
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 9
8
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: nqo9
EC: 1.6.5.11
Find proteins for Q56224 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56224
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL
A, a
446Bos taurusGene Names: UQCRC1
Find proteins for P31800 (Bos taurus)
Go to Gene View: UQCRC1
Go to UniProtKB:  P31800
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL
B, b
439Bos taurusGene Names: UQCRC2
Find proteins for P23004 (Bos taurus)
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Go to UniProtKB:  P23004
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B
C, c
379Bos taurusGene Names: MT-CYB (COB, CYTB, MTCYB)
Find proteins for P00157 (Bos taurus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P00157
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
D, d
241Bos taurusGene Names: CYC1
Find proteins for P00125 (Bos taurus)
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Go to UniProtKB:  P00125
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
E, e
196Bos taurusGene Names: UQCRFS1
EC: 1.10.2.2
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 7
F, f
110Bos taurusGene Names: UQCRB
Find proteins for P00129 (Bos taurus)
Go to Gene View: UQCRB
Go to UniProtKB:  P00129
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 8
G, g
81Bos taurusGene Names: UQCRQ
Find proteins for P13271 (Bos taurus)
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Go to UniProtKB:  P13271
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIAL
H, h
78Bos taurusGene Names: UQCRH
Find proteins for P00126 (Bos taurus)
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Go to UniProtKB:  P00126
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
I, i
65Bos taurusGene Names: UQCRFS1
EC: 1.10.2.2
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 9
J, j
62Bos taurusGene Names: UQCR10
Find proteins for P00130 (Bos taurus)
Go to Gene View: UQCR10
Go to UniProtKB:  P00130
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B-C1 COMPLEX SUBUNIT 10
K, k
56Bos taurusGene Names: UQCR11 (UQCR)
Find proteins for P07552 (Bos taurus)
Go to Gene View: UQCR11
Go to UniProtKB:  P07552
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 1
L
514Bos taurusGene Names: MT-CO1 (COI, COXI, MTCO1)
EC: 1.9.3.1
Find proteins for P00396 (Bos taurus)
Go to Gene View: MT-CO1
Go to UniProtKB:  P00396
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 2
M
227Bos taurusGene Names: MT-CO2 (COII, COXII, MTCO2)
Find proteins for P68530 (Bos taurus)
Go to Gene View: MT-CO2
Go to UniProtKB:  P68530
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 3
N
261Bos taurusGene Names: MT-CO3 (COIII, COXIII, MTCO3)
Find proteins for P00415 (Bos taurus)
Go to Gene View: MT-CO3
Go to UniProtKB:  P00415
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1, MITOCHONDRIAL
O
147Bos taurusGene Names: COX4I1 (COX4)
Find proteins for P00423 (Bos taurus)
Go to Gene View: COX4I1
Go to UniProtKB:  P00423
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 5A, MITOCHONDRIAL
P
109Bos taurusGene Names: COX5A
Find proteins for P00426 (Bos taurus)
Go to Gene View: COX5A
Go to UniProtKB:  P00426
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIAL
Q
98Bos taurusGene Names: COX5B
Find proteins for P00428 (Bos taurus)
Go to Gene View: COX5B
Go to UniProtKB:  P00428
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE POLYPEPTIDE VIA, CYTOCHROME C OXIDASE POLYPEPTIDE VB
R
84Bos taurusGene Names: COX6A2 (COX6A)
Find proteins for P07471 (Bos taurus)
Go to Gene View: COX6A2
Go to UniProtKB:  P07471
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 6B1
S
85Bos taurusGene Names: COX6B1 (COX6B)
Find proteins for P00429 (Bos taurus)
Go to Gene View: COX6B1
Go to UniProtKB:  P00429
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 6C
T
73Bos taurusGene Names: COX6C
Find proteins for P04038 (Bos taurus)
Go to Gene View: COX6C
Go to UniProtKB:  P04038
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 7A1, MITOCHONDRIAL
U
59Bos taurusGene Names: COX7A1 (COX7A, COX7AH)
Find proteins for P07470 (Bos taurus)
Go to Gene View: COX7A1
Go to UniProtKB:  P07470
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 7B, MITOCHONDRIAL
V
56Bos taurusGene Names: COX7B
Find proteins for P13183 (Bos taurus)
Go to Gene View: COX7B
Go to UniProtKB:  P13183
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 7C, MITOCHONDRIAL
W
47Bos taurusGene Names: COX7C (COX7CP1)
Find proteins for P00430 (Bos taurus)
Go to Gene View: COX7C
Go to UniProtKB:  P00430
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE SUBUNIT 8B, MITOCHONDRIAL
X
46Bos taurusGene Names: COX8B (COX8H)
Find proteins for P10175 (Bos taurus)
Go to UniProtKB:  P10175
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
Y
104Bos taurusGene Names: CYCS (CYC)
Find proteins for P62894 (Bos taurus)
Go to Gene View: CYCS
Go to UniProtKB:  P62894
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT L,
m
474N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT M,
n
391N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT N
o
378N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
NADH-QUINONE OXIDOREDUCTASE SUBUNIT K
p
281N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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L
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
SF4
Query on SF4

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1, 3, 6, 8
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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Q
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CDL
Query on CDL

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d, G, g
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ1
Query on UQ1

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C, c
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

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1
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
CA
Query on CA

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7
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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2, 3, E, e
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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1, 2, 3, 4, 5, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

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1
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
HEM
Query on HEM

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c, C, Y
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CU
Query on CU

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L, M
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

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d, D
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SMA
Query on SMA

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C, c
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
m, n, o, p
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Other
  • Version 1.2: 2017-08-30
    Type: Advisory, Data collection