3CXH

Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

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Literature

Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.

Solmaz, S.R., Hunte, C.

(2008) J Biol Chem 283: 17542-17549

  • DOI: 10.1074/jbc.M710126200
  • Primary Citation of Related Structures:  
    3CX5, 3CXH

  • PubMed Abstract: 

    • In cellular respiration, cytochrome c transfers electrons from cytochrome bc(1) complex (complex III) to cytochrome c oxidase by transiently binding to the membrane proteins. Here, we report the structure of isoform-1 cytochrome c bound to cytochrome ...

    In cellular respiration, cytochrome c transfers electrons from cytochrome bc(1) complex (complex III) to cytochrome c oxidase by transiently binding to the membrane proteins. Here, we report the structure of isoform-1 cytochrome c bound to cytochrome bc(1) complex at 1.9 A resolution in reduced state. The dimer structure is asymmetric. Monovalent cytochrome c binding is correlated with conformational changes of the Rieske head domain and subunit QCR6p and with a higher number of interfacial water molecules bound to cytochrome c(1). Pronounced hydration and a "mobility mismatch" at the interface with disordered charged residues on the cytochrome c side are favorable for transient binding. Within the hydrophobic interface, a minimal core was identified by comparison with the novel structure of the complex with bound isoform-2 cytochrome c. Four core interactions encircle the heme cofactors surrounded by variable interactions. The core interface may be a feature to gain specificity for formation of the reactive complex.

    Organizational Affiliation: 

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA, L431Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB, M352Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC, N385Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD, O248Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE, P185Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6F, Q146Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7G, R126Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8H, S93Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 9
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Cytochrome b-c1 complex subunit 9I, T65Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN (VH) OF FV-FRAGMENTJ, U127Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT CHAIN (VL) OF FV-FRAGMENTK, V107Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c iso-2W112Saccharomyces cerevisiaeMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 13
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
X
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CN6
Query on CN6
Download Ideal Coordinates CCD File 
C, N
(2R,5R,11S,14R)-2-(butanoyloxy)-5,8,11-trihydroxy-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
C31 H58 O17 P2
OCYQEYZGHKBQOW-ZONZVBGPSA-N		 Ligand Interaction
8PE
Query on 8PE
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C, N
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N		 Ligand Interaction
HEM
Query on HEM
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C, D, N, O, W
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
9PE
Query on 9PE
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C, N
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N		 Ligand Interaction
6PH
Query on 6PH
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E, L
(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
C31 H61 O8 P
UOOPRMYYAWVCCZ-GDLZYMKVSA-N		 Ligand Interaction
7PH
Query on 7PH
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D, O
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
C29 H57 O8 P
UYOIGTVMJVHOSC-HHHXNRCGSA-N		 Ligand Interaction
SMA
Query on SMA
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C, N
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N		 Ligand Interaction
UMQ
Query on UMQ
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A, L
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N		 Ligand Interaction
FES
Query on FES
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E, P
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L		WL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 13
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003		XsucroseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.54α = 90
b = 162.97β = 104.39
c = 194.23γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DNAdata collection
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-09-25
    Changes: Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary