3KMF

Room Temperature Time-of-Flight Neutron Diffraction Study of Deoxy Human Normal Adult Hemoglobin


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Direct Determination of Protonation States of Histidine Residues in a 2 A Neutron Structure of Deoxy-Human Normal Adult Hemoglobin and Implications for the Bohr Effect.

Kovalevsky, A.Y.Chatake, T.Shibayama, N.Park, S.Y.Ishikawa, T.Mustyakimov, M.Fisher, Z.Langan, P.Morimoto, Y.

(2010) J.Mol.Biol. 398: 276-291

  • DOI: 10.1016/j.jmb.2010.03.016

  • PubMed Abstract: 
  • We have investigated the protonation states of histidine residues (potential Bohr groups) in the deoxy form (T state) of human hemoglobin by direct determination of hydrogen (deuterium) positions with the neutron protein crystallography technique. Th ...

    We have investigated the protonation states of histidine residues (potential Bohr groups) in the deoxy form (T state) of human hemoglobin by direct determination of hydrogen (deuterium) positions with the neutron protein crystallography technique. The reversible binding of protons is key to the allosteric regulation of human hemoglobin. The protonation states of 35 of the 38 His residues were directly determined from neutron scattering omit maps, with 3 of the remaining residues being disordered. Protonation states of 5 equivalent His residues--alpha His20, alpha His50, alpha His89, beta His143, and beta His146--differ between the symmetry-related globin subunits. The distal His residues, alpha His58 and beta His63, are protonated in the alpha 1 beta 1 heterodimer and are neutral in alpha 2 beta 2. Buried residue alpha His103 is found to be protonated in both subunits. These distal and buried residues have the potential to act as Bohr groups. The observed protonation states of His residues are compared to changes in their pK(a) values during the transition from the T to the R state and the results provide some new insights into our understanding of the molecular mechanism of the Bohr effect.


    Organizational Affiliation

    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. ayk@lanl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A, E
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
C, G
146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 
Software Package:
Software NamePurpose
LAUENORMdata scaling
nCNSphasing
d*TREKdata reduction
nCNSrefinement
PCSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2018-06-13
    Type: Atomic model, Data collection