1J41

Direct observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Ni)-beta(Fe) hemoglobin (laser photolysed)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Direct observation of photolysis-induced tertiary structural changes in hemoglobin

Adachi, S.Park, S.-Y.Tame, J.R.H.Shiro, Y.Shibayama, N.

(2003) Proc.Natl.Acad.Sci.USA 100: 7039-7044

  • DOI: 10.1073/pnas.1230629100
  • Primary Citation of Related Structures:  1J3Y, 1J3Z, 1J40

  • PubMed Abstract: 
  • Human Hb, an alpha2beta2 tetrameric oxygen transport protein that switches from a T (tense) to an R (relaxed) quaternary structure during oxygenation, has long served as a model for studying protein allostery in general. Time-resolved spectroscopic m ...

    Human Hb, an alpha2beta2 tetrameric oxygen transport protein that switches from a T (tense) to an R (relaxed) quaternary structure during oxygenation, has long served as a model for studying protein allostery in general. Time-resolved spectroscopic measurements after photodissociation of CO-liganded Hb have played a central role in exploring both protein dynamical responses and molecular cooperativity, but the direct visualization and the structural consequences of photodeligation have not yet been reported. Here we present an x-ray study of structural changes induced by photodissociation of half-liganded T-state and fully liganded R-state human Hb at cryogenic temperatures (25-35 K). On photodissociation of CO, structural changes involving the heme and the F-helix are more marked in the alpha subunit than in the beta subunit, and more subtle in the R state than in the T state. Photodeligation causes a significant sliding motion of the T-state beta heme. Our results establish that the structural basis of the low affinity of the T state is radically different between the subunits, because of differences in the packing and chemical tension at the hemes.


    Organizational Affiliation

    RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148, Japan. sadachi@spring8.or.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha Chain
A, C, E, G
141Homo sapiensGene 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 beta Chain
B, D, F, H
146Homo sapiensGene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2FU
Query on 2FU

Download SDF File 
Download CCD File 
B, F
BUT-2-ENEDIAL
C4 H4 O2
JGEMYUOFGVHXKV-OWOJBTEDSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
B, D, F, H
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
HNI
Query on HNI

Download SDF File 
Download CCD File 
A, C, E, G
PROTOPORPHYRIN IX CONTAINING NI(II)
C34 H32 N4 Ni O4
IJROJBFZULUEEG-QFCVZVLGDG
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.542α = 90.00
b = 94.565β = 101.84
c = 99.449γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance