3CX5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrialA, L431N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 2, mitochondrialB, M352N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME BC, N385N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrialD, O248N/AMutation(s): 0 
EC: 1.10.2.2
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrialE, P185N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 6F, Q146N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 7G, R126N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 8H, S93N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 9I, T65N/AMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
HEAVY CHAIN (VH) OF FV-FRAGMENTJ, U127Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
LIGHT CHAIN (VL) OF FV-FRAGMENTK, V107Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c iso-1W108N/AMutation(s): 0 
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  • Reference Sequence
Oligosaccharides
Entity ID: 13
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
X
2 N/A
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CN3
Query on CN3

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D, N
(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
C36 H68 O17 P2
FMNZIMGRZPIVKW-XWHIBYANSA-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
CN5
Query on CN5

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C
(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
C26 H52 O13 P2
UKWPDXFRXMWSMQ-VWLOTQADSA-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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A, 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.12α = 90
b = 165.09β = 104.09
c = 194.37γ = 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