2FYN | pdb_00002fyn

Crystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.254 (Depositor) 
  • R-Value Work: 
    0.224 (Depositor) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex.

Esser, L.Gong, X.Yang, S.Yu, L.Yu, C.A.Xia, D.

(2006) Proc Natl Acad Sci U S A 103: 13045-13050

  • DOI: https://doi.org/10.1073/pnas.0601149103
  • Primary Citation Related Structures: 
    2FYN, 2FYU

  • PubMed Abstract: 

    In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is controlled so that only one electron enters the thermodynamically favorable chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound Q(o) site inhibitors revealed that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP. The analysis also suggests a mechanism for reversal of the ISP fixation when the shape complementarity is significantly reduced after a positional reorientation of the reaction product quinone. The importance of shape complementarity in this mechanism was confirmed by functional studies of bc(1) mutants and by a structure determination of the bacterial form of bc(1). A mechanism for the high fidelity of the bifurcated electron transfer is proposed.


  • Organizational Affiliation
    • Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 615.9 kDa 
  • Atom Count: 41,688 
  • Modeled Residue Count: 5,178 
  • Deposited Residue Count: 5,406 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b
A, D, G, J, M
A, D, G, J, M, P
445Cereibacter sphaeroidesMutation(s): 1 
Gene Names: petBfbcB
Membrane Entity: Yes 
UniProt
Find proteins for Q02761 (Cereibacter sphaeroides)
Explore Q02761 
Go to UniProtKB:  Q02761
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02761
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1
B, E, H, K, N
B, E, H, K, N, Q
269Cereibacter sphaeroidesMutation(s): 0 
Gene Names: petCfbcC
Membrane Entity: Yes 
UniProt
Find proteins for Q02760 (Cereibacter sphaeroides)
Explore Q02760 
Go to UniProtKB:  Q02760
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02760
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit
C, F, I, L, O
C, F, I, L, O, R
187Cereibacter sphaeroidesMutation(s): 1 
Gene Names: petAfbcF
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q02762 (Cereibacter sphaeroides)
Explore Q02762 
Go to UniProtKB:  Q02762
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02762
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LOP

Query on LOP



Download:Ideal Coordinates CCD File
BA [auth D]
HA [auth G]
NA [auth J]
TA [auth M]
V [auth A]
BA [auth D],
HA [auth G],
NA [auth J],
TA [auth M],
V [auth A],
ZA [auth P]
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
AB [auth Q]
CA [auth E]
EA [auth G]
FA [auth G]
IA [auth H]
AB [auth Q],
CA [auth E],
EA [auth G],
FA [auth G],
IA [auth H],
KA [auth J],
LA [auth J],
OA [auth K],
QA [auth M],
RA [auth M],
S [auth A],
T [auth A],
UA [auth N],
W [auth B],
WA [auth P],
XA [auth P],
Y [auth D],
Z [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SMA

Query on SMA



Download:Ideal Coordinates CCD File
AA [auth D]
GA [auth G]
MA [auth J]
SA [auth M]
U [auth A]
AA [auth D],
GA [auth G],
MA [auth J],
SA [auth M],
U [auth A],
YA [auth P]
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
BB [auth R]
DA [auth F]
JA [auth I]
PA [auth L]
VA [auth O]
BB [auth R],
DA [auth F],
JA [auth I],
PA [auth L],
VA [auth O],
X [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.254 (Depositor) 
  • R-Value Work:  0.224 (Depositor) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 351.3α = 90
b = 147.13β = 103.94
c = 160.83γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary