5C6E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.301 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 ...

    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.,Sect.D 65: 567


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A
141Equus caballusMutation(s): 0 
Gene Names: HBA
Find proteins for P01958 (Equus caballus)
Go to UniProtKB:  P01958
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B
146Equus caballusMutation(s): 0 
Gene Names: HBB
Find proteins for P02062 (Equus caballus)
Go to Gene View: HBB
Go to UniProtKB:  P02062
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A, B
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A, B
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.860α = 90.00
b = 63.160β = 110.75
c = 54.710γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.301 
Software Package:
Software NamePurpose
CNSphasing
MOSFLMdata reduction
nCNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM071939-01
National Science Foundation (United States)United States446218

Revision History 

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