3OO5

R-state human hemoglobin: nitriheme modified

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystallographic Trapping of Heme Loss Intermediates during the Nitrite-Induced Degradation of Human Hemoglobin.

Yi, J., Thomas, L.M., Musayev, F.N., Safo, M.K., Richter-Addo, G.B.

(2011) Biochemistry 50: 8323-8332

  • DOI: 10.1021/bi2009322
  • Primary Citation of Related Structures:  
    3ONZ, 3OO4, 3OO5

  • PubMed Abstract: 

    • Heme is an important cofactor in a large number of essential proteins and is often involved in small molecule binding and activation. Loss of heme from proteins thus negatively affects the function of these proteins but is also an important component ...

    Heme is an important cofactor in a large number of essential proteins and is often involved in small molecule binding and activation. Loss of heme from proteins thus negatively affects the function of these proteins but is also an important component of iron recycling. The characterization of intermediates that form during the loss of heme from proteins has been problematic, in a large part, because of the instability of such intermediates. We have characterized, by X-ray crystallography, three compounds that form during the nitrite-induced degradation of human α(2)β(2) hemoglobin (Hb). The first is an unprecedented complex that exhibits a large β heme displacement of 4.8 Å toward the protein exterior; the heme displacement is stabilized by the binding of the distal His residue to the heme Fe, which in turn allows for the unusual binding of an exogenous ligand on the proximal face of the heme. We have also structurally characterized complexes that display regiospecific nitration of the heme at the 2-vinyl position; we show that heme nitration is not a prerequisite for heme loss. Our results provide structural insight into a possible pathway for nitrite-induced loss of heme from human Hb.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States. yijun@ou.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit alphaA141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
NIH Common Fund Data Resources
PHAROS  P69905
GTEx  ENSG00000188536GTEx  ENSG00000206172
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit betaB146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
NIH Common Fund Data Resources
PHAROS  P68871
GTEx  ENSG00000244734
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NTE
Query on NTE
Download CCD File 
A, B
[3,3'-{7-ethenyl-3,8,13,17-tetramethyl-12-[(E)-2-nitroethenyl]porphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~}dipro panoato(2-)]iron
C34 H31 Fe N5 O6
MBEUICWDKPMPCN-RXJYIKGQSA-L		 Ligand Interaction
NO2
Query on NO2
Download CCD File 
A
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.499α = 90
b = 53.499β = 90
c = 192.221γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references