Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 129385.68 
• Atom Count: 9132 
• Residue Count: 1148 
• Unique protein chains: 2

1J40

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

• DOI: 10.2210/pdb1J40/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Homo sapiens


• Deposited: 2003-02-21 Released: 2003-07-22 
• Deposition Author(s): Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 

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

• PubMed: 12773618 
• DOI: 10.1073/pnas.1230629100
• Primary Citation of Related Structures:  
  1J41, 1J3Z, 1J3Y


• 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 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.

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Organizational Affiliation: 

RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin alpha Chain	A, C, E, G	141	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin beta Chain	B, D, F, H	146	Homo sapiens	Mutation(s): 0  Gene Names: HBB
Find proteins for P68871 (Homo sapiens) Go to Gene View: HBB Go to UniProtKB:  P68871

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
2FU	D, F	BUT-2-ENEDIAL C4 H4 O2 JGEMYUOFGVHXKV-OWOJBTEDSA-N
HEM	B, D, F, H	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	B, D, F, H	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
HNI	A, C, E, G	PROTOPORPHYRIN IX CONTAINING NI(II) C34 H32 N4 Ni O4 IJROJBFZULUEEG-QFCVZVLGDG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 64.708	α = 90.00
b = 94.860	β = 101.97
c = 99.730	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-21 
• Released Date: 2003-07-22 
• Deposition Author(s): Adachi, S., Park, S.-Y., Tame, J.R.H., Shiro, Y., Shibayama, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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