2YBB

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1038/emboj.2011.324
  • Primary Citation of Related Structures:  
    2YBB

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 1A [auth 1]438Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 2B [auth 2]181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 3C [auth 3]783Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 4D [auth 4]409Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 5E [auth 5]207Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 6F [auth 6]181Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 15G [auth 7]129Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT 9H [auth 8]182Thermus thermophilus HB8Mutation(s): 0 
EC: 1.6.99.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIALHA [auth a],
I [auth A]
446Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIALIA [auth b],
J [auth B]
439Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME BJA [auth c],
K [auth C]
379Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIALKA [auth d],
L [auth D]
241Bos taurusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIALLA [auth e],
M [auth E]
196Bos taurusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 7MA [auth f],
N [auth F]
110Bos taurusMutation(s): 1 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 8NA [auth g],
O [auth G]
81Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 6, MITOCHONDRIALOA [auth h],
P [auth H]
78Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIALPA [auth i],
Q [auth I]
65Bos taurusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 9QA [auth j],
R [auth J]
62Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B-C1 COMPLEX SUBUNIT 10RA [auth k],
S [auth K]
56Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 1T [auth L]514Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 2U [auth M]227Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 3V [auth N]261Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1, MITOCHONDRIALW [auth O]147Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 5A, MITOCHONDRIALX [auth P]109Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 5B, MITOCHONDRIALY [auth Q]98Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE POLYPEPTIDE VIA, CYTOCHROME C OXIDASE POLYPEPTIDE VBZ [auth R]84Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 6B1AA [auth S]85Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 6CBA [auth T]73Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 7A1, MITOCHONDRIALCA [auth U]59Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 7B, MITOCHONDRIALDA [auth V]56Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 7C, MITOCHONDRIALEA [auth W]47Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASE SUBUNIT 8B, MITOCHONDRIALFA [auth X]46Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME CGA [auth Y]104Bos taurusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT L,SA [auth m]474Escherichia coli BL21Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT M,TA [auth n]391Escherichia coli BL21Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT NUA [auth o]378Escherichia coli BL21Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-QUINONE OXIDOREDUCTASE SUBUNIT KVA [auth p]281Escherichia coli BL21Mutation(s): 0 
EC: 1.6.5.3
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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JC [auth d],
LC [auth g],
UB [auth G],
VB [auth G]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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WB [auth L],
XB [auth L]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
NAI
Query on NAI

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YA [auth 1]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
HEC
Query on HEC

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IC [auth d],
SB [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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DC [auth Y],
EC [auth c],
FC [auth c],
OB [auth C],
PB [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SMA
Query on SMA

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GC [auth c],
QB [auth C]
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
FMN
Query on FMN

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XA [auth 1]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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CB [auth 3]
DB [auth 3]
EB [auth 3]
KB [auth 6]
MB [auth 8]
CB [auth 3],
DB [auth 3],
EB [auth 3],
KB [auth 6],
MB [auth 8],
NB [auth 8],
WA [auth 1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UQ1
Query on UQ1

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HC [auth c],
RB [auth C]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
FES
Query on FES

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AB [auth 2],
FB [auth 3],
KC [auth e],
TB [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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CC [auth Q]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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AC [auth M],
BC [auth M],
YB [auth L]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

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LB [auth 7]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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BB [auth 2]
GB [auth 3]
HB [auth 3]
IB [auth 4]
JB [auth 5]
BB [auth 2],
GB [auth 3],
HB [auth 3],
IB [auth 4],
JB [auth 5],
ZA [auth 1],
ZB [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMAGIC
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Other
  • Version 1.2: 2017-08-30
    Changes: Advisory, Data collection
  • Version 1.3: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary