2J7A

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

X-Ray Structure of the Membrane-Bound Cytochrome C Quinol Dehydrogenase Nrfh Reveals Novel Haem Coordination.

Rodrigues, M.L.Oliveira, T.F.Pereira, I.A.C.Archer, M.

(2006) EMBO J 25: 5951

  • DOI: https://doi.org/10.1038/sj.emboj.7601439
  • Primary Citation of Related Structures:  
    2J7A

  • PubMed Abstract: 

    Oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate ATP by oxidative phosphorylation. A novel family of cytochrome c quinol dehydrogenases that play an important role in bacterial respiratory chains was recognised in recent years. Here, we describe the first structure of a cytochrome from this family, NrfH from Desulfovibrio vulgaris, which forms a stable complex with its electron partner, the cytochrome c nitrite reductase NrfA. One NrfH molecule interacts with one NrfA dimer in an asymmetrical manner, forming a large membrane-bound complex with an overall alpha(4)beta(2) quaternary arrangement. The menaquinol-interacting NrfH haem is pentacoordinated, bound by a methionine from the CXXCHXM sequence, with an aspartate residue occupying the distal position. The NrfH haem that transfers electrons to NrfA has a lysine residue from the closest NrfA molecule as distal ligand. A likely menaquinol binding site, containing several conserved and essential residues, is identified.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, ITQB-UNL, Oeiras, Portugal.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C NITRITE REDUCTASE NRFA
A, B, D, E, G
A, B, D, E, G, H, J, K, M, N, P, Q
500Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
EC: 1.7.2.2
Membrane Entity: Yes 
UniProt
Find proteins for Q72EF3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72EF3 
Go to UniProtKB:  Q72EF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72EF3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C QUINOL DEHYDROGENASE NRFH
C, F, I, L, O
C, F, I, L, O, R
159Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q72EF4 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72EF4 
Go to UniProtKB:  Q72EF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72EF4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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AA [auth B]
AB [auth F]
AC [auth J]
AD [auth N]
AE [auth R]
AA [auth B],
AB [auth F],
AC [auth J],
AD [auth N],
AE [auth R],
BA [auth B],
BB [auth F],
BC [auth J],
BD [auth N],
BE [auth R],
CA [auth B],
CB [auth F],
CC [auth J],
CD [auth N],
CE [auth R],
DA [auth B],
DB [auth F],
DC [auth J],
DD [auth N],
DE [auth R],
FB [auth G],
GA [auth C],
GB [auth G],
GC [auth K],
GD [auth O],
HA [auth C],
HB [auth G],
HC [auth K],
HD [auth O],
IA [auth C],
IB [auth G],
IC [auth K],
ID [auth O],
JA [auth C],
JB [auth G],
JC [auth K],
JD [auth O],
KC [auth K],
MA [auth D],
MB [auth H],
MD [auth P],
NA [auth D],
NB [auth H],
NC [auth L],
ND [auth P],
OA [auth D],
OB [auth H],
OC [auth L],
OD [auth P],
PA [auth D],
PB [auth H],
PC [auth L],
PD [auth P],
QA [auth D],
QB [auth H],
QD [auth P],
RC [auth L],
S [auth A],
SC [auth M],
T [auth A],
TA [auth E],
TB [auth I],
TC [auth M],
TD [auth Q],
U [auth A],
UA [auth E],
UB [auth I],
UC [auth M],
UD [auth Q],
V [auth A],
VA [auth E],
VB [auth I],
VC [auth M],
VD [auth Q],
W [auth A],
WA [auth E],
WB [auth I],
WC [auth M],
WD [auth Q],
XA [auth E],
XD [auth Q],
Z [auth B],
ZB [auth J],
ZC [auth N]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
LMT
Query on LMT

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EB [auth F]
EE [auth R]
KA [auth C]
KD [auth O]
QC [auth L]
EB [auth F],
EE [auth R],
KA [auth C],
KD [auth O],
QC [auth L],
XB [auth I]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ACT
Query on ACT

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LA [auth C],
LD [auth O],
YB [auth I]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

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EA [auth B]
EC [auth J]
ED [auth N]
FA [auth B]
FC [auth J]
EA [auth B],
EC [auth J],
ED [auth N],
FA [auth B],
FC [auth J],
FD [auth N],
KB [auth G],
LB [auth G],
LC [auth K],
MC [auth K],
RA [auth D],
RB [auth H],
RD [auth P],
SA [auth D],
SB [auth H],
SD [auth P],
X [auth A],
XC [auth M],
Y [auth A],
YA [auth E],
YC [auth M],
YD [auth Q],
ZA [auth E],
ZD [auth Q]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.664α = 90
b = 258.117β = 90
c = 580.742γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-06
    Type: Initial release
  • Version 2.0: 2019-09-25
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary
  • Version 2.1: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary