5C6E

Joint X-ray/neutron structure of equine cyanomet hemoglobin in R state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.301 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Visualizing the Bohr effect in hemoglobin: neutron structure of equine cyanomethemoglobin in the R state and comparison with human deoxyhemoglobin in the T state.

Dajnowicz, S.Seaver, S.Hanson, B.L.Fisher, S.Z.Langan, P.Kovalevsky, A.Y.Mueser, T.C.

(2016) Acta Crystallogr D Struct Biol 72: 892-903

  • DOI: 10.1107/S2059798316009049
  • Primary Citation of Related Structures:  
    5C6E

  • PubMed Abstract: 
  • Neutron crystallography provides direct visual evidence of the atomic positions of deuterium-exchanged H atoms, enabling the accurate determination of the protonation/deuteration state of hydrated biomolecules. Comparison of two neutron structures of hemoglobins, human deoxyhemoglobin (T state) and equine cyanomethemoglobin (R state), offers a direct observation of histidine residues that are likely to contribute to the Bohr effect ...

    Neutron crystallography provides direct visual evidence of the atomic positions of deuterium-exchanged H atoms, enabling the accurate determination of the protonation/deuteration state of hydrated biomolecules. Comparison of two neutron structures of hemoglobins, human deoxyhemoglobin (T state) and equine cyanomethemoglobin (R state), offers a direct observation of histidine residues that are likely to contribute to the Bohr effect. Previous studies have shown that the T-state N-terminal and C-terminal salt bridges appear to have a partial instead of a primary overall contribution. Four conserved histidine residues [αHis72(EF1), αHis103(G10), αHis89(FG1), αHis112(G19) and βHis97(FG4)] can become protonated/deuterated from the R to the T state, while two histidine residues [αHis20(B1) and βHis117(G19)] can lose a proton/deuteron. αHis103(G10), located in the α1:β1 dimer interface, appears to be a Bohr group that undergoes structural changes: in the R state it is singly protonated/deuterated and hydrogen-bonded through a water network to βAsn108(G10) and in the T state it is doubly protonated/deuterated with the network uncoupled. The very long-term H/D exchange of the amide protons identifies regions that are accessible to exchange as well as regions that are impermeable to exchange. The liganded relaxed state (R state) has comparable levels of exchange (17.1% non-exchanged) compared with the deoxy tense state (T state; 11.8% non-exchanged). Interestingly, the regions of non-exchanged protons shift from the tetramer interfaces in the T-state interface (α1:β2 and α2:β1) to the cores of the individual monomers and to the dimer interfaces (α1:β1 and α2:β2) in the R state. The comparison of regions of stability in the two states allows a visualization of the conservation of fold energy necessary for ligand binding and release.


    Related Citations: 
    • Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
      Adams, P.D., Mustyakimov, M., Afonine, P.V., Langan, P.
      (2009) Acta Crystallogr D Biol Crystallogr 65: 567

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit alphaA141Equus caballusMutation(s): 0 
Gene Names: HBA
UniProt
Find proteins for P01958 (Equus caballus)
Explore P01958 
Go to UniProtKB:  P01958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01958
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit betaB146Equus caballusMutation(s): 0 
Gene Names: HBB
UniProt
Find proteins for P02062 (Equus caballus)
Explore P02062 
Go to UniProtKB:  P02062
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02062
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CYN
Query on CYN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.301 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.86α = 90
b = 63.16β = 110.75
c = 54.71γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
nCNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM071939-01
National Science Foundation (NSF, United States)United States446218

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.3: 2018-04-25
    Changes: Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence