Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.08 kDa 
• Atom Count: 2979 
• Residue Count: 271 
• Unique protein chains: 1

1UMK

The Structure of Human Erythrocyte NADH-cytochrome b5 Reductase

• DOI: 10.2210/pdb1UMK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-03 Released: 2004-11-02 
• Deposition Author(s): Bando, S., Takano, T., Yubisui, T., Shirabe, K., Takeshita, M., Horii, C., Nakagawa, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.207 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Structure of human erythrocyte NADH-cytochrome b5 reductase.

Bando, S., Takano, T., Yubisui, T., Shirabe, K., Takeshita, M., Nakagawa, A.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1929-1934

• PubMed: 15502298 
• DOI: 10.1107/S0907444904020645
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Erythrocyte NADH-cytochrome b(5) reductase reduces methaemoglobin to functional haemoglobin. In order to examine the function of the enzyme, the structure of NADH-cytochrome b(5) reductase from human erythrocytes has been determined and refined by X-ray crystallography. At 1.75 A resolution, the root-mean-square deviations (r.m.s.d.) from standard bond lengths and angles are 0.006 A and 1.03 degrees , respectively. The molecular structure was compared with those of rat NADH-cytochrome b(5) reductase and corn nitrate reductase. The human reductase resembles the rat reductase in overall structure as well as in many side chains. Nevertheless, there is a large main-chain shift from the human reductase to the rat reductase or the corn reductase caused by a single-residue replacement from proline to threonine. A model of the complex between cytochrome b(5) and the human reductase has been built and compared with that of the haem-containing domain of the nitrate reductase molecule. The interaction between cytochrome b(5) and the human reductase differs from that of the nitrate reductase because of differences in the amino-acid sequences. The structures around 15 mutation sites of the human reductase have been examined for the influence of residue substitutions using the program ROTAMER. Five mutations in the FAD-binding domain seem to be related to cytochrome b(5).

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Organizational Affiliation: 

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NADH-cytochrome b5 reductase	A	275	Homo sapiens	Mutation(s): 0  Gene Names: CYB5R3, DIA1 EC: 1.6.2.2
Find proteins for P00387 (Homo sapiens) Go to UniProtKB:  P00387
NIH Common Fund Data Resources
PHAROS  P00387 GTEx  ENSG00000100243

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.207 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.869	α = 90
b = 65.869	β = 90
c = 76.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-03 
• Released Date: 2004-11-02 
Deposition Author(s): Bando, S., Takano, T., Yubisui, T., Shirabe, K., Takeshita, M., Horii, C., Nakagawa, A.

Revision History 

• Version 1.0: 2004-11-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance