Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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)

Macromolecule Content

• Total Structure Weight: 64.55 kDa 
• Atom Count: 4745 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

1XZ2

wild-type hemoglobin deoxy no-salt

• PDB DOI: 10.2210/pdb1XZ2/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2004-11-11 Released: 2004-11-30 
• Deposition Author(s): Kavanaugh, J.S., Rogers, P.H., Arnone, A., Hui, H.L., Wierzba, A., DeYoung, A., Kwiatkowski, L.D., Noble, R.W., Juszczak, L.J., Peterson, E.S., Friedman, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Literature

Intersubunit interactions associated with tyr42alpha stabilize the quaternary-T tetramer but are not major quaternary constraints in deoxyhemoglobin

Kavanaugh, J.S., Rogers, P.H., Arnone, A., Hui, H.L., Wierzba, A., Deyoung, A., Kwiatkowski, L.D., Noble, R.W., Juszczak, L.J., Peterson, E.S., Friedman, J.M.

(2005) Biochemistry 44: 3806-3820

• PubMed: 15751957 
• DOI: 10.1021/bi0484670
• Primary Citation of Related Structures:  
  1XYE, 1XZ2, 1XZ4


• PubMed Abstract: 
  

Previous mutational studies on Tyr42alpha variants as well as the current studies on the mutant hemoglobin alphaY42A show that the intersubunit interactions associated with Tyr42alpha significantly stabilize the alpha1beta2 interface of the quaternary-T deoxyhemoglobin tetramer. However, crystallographic studies, UV and visible resonance Raman spectroscopy, CO combination kinetic measurements, and oxygen binding measurements on alphaY42A show that the intersubunit interactions formed by Tyr42alpha have only a modest influence on the structural properties and ligand affinity of the deoxyhemoglobin tetramer. Therefore, the alpha1beta2 interface interactions associated with Tyr42alpha do not contribute significantly to the quaternary constraints that are responsible for the low oxygen affinity of deoxyhemoglobin. The slight increase in the ligand affinity of deoxy alphaY42A correlates with small, mutation-induced structural changes that perturb the environment of Trp37beta, a critical region of the quaternary-T alpha1beta2 interface that has been shown to be the major source of quaternary constraint in deoxyhemoglobin.

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Organizational Affiliation: 

Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin alpha chain	A, C	141	Homo sapiens	Mutation(s): 0  Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin beta chain	B, D	146	Homo sapiens	Mutation(s): 0  Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.9	α = 90
b = 112.1	β = 90
c = 63.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SDMS	data reduction
SDMS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-11-11 
• Released Date: 2004-11-30 
Deposition Author(s): Kavanaugh, J.S., Rogers, P.H., Arnone, A., Hui, H.L., Wierzba, A., DeYoung, A., Kwiatkowski, L.D., Noble, R.W., Juszczak, L.J., Peterson, E.S., Friedman, J.M.

Revision History  

• Version 1.0: 2004-11-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance