Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.38 kDa 
• Atom Count: 2366 
• Modelled Residue Count: 282 
• Deposited Residue Count: 282 
• Unique protein chains: 1

1ITH

STRUCTURE DETERMINATION AND REFINEMENT OF HOMOTETRAMERIC HEMOGLOBIN FROM URECHIS CAUPO AT 2.5 ANGSTROMS RESOLUTION

• PDB DOI: 10.2210/pdb1ITH/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Urechis caupo
• Mutation(s): No 


• Deposited: 1991-12-03 Released: 1993-10-31 
• Deposition Author(s): Hackert, M., Kolatkar, P., Ernst, S.R., Ogata, C.M., Hendrickson, W.A., Merritt, E.A., Phizackerley, R.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.147 
• R-Value Observed: 0.147 

Literature

Structure determination and refinement of homotetrameric hemoglobin from Urechis caupo at 2.5 A resolution.

Kolatkar, P.R., Ernst, S.R., Hackert, M.L., Ogata, C.M., Hendrickson, W.A., Merritt, E.A., Phizackerley, R.P.

(1992) Acta Crystallogr B 48: 191-199

• PubMed: 1515107 
• DOI: 10.1107/s0108768191012363
• Primary Citation of Related Structures:  
  1ITH


• PubMed Abstract: 
  

A 5 A resolution multiple isomorphous replacement solution for hemoglobin isolated from Urechis caupo revealed a previously unobserved quaternary structure for tetrameric hemoglobin [Kolatkar, Meador, Stanfield & Hackert (1988). J. Biol. Chem. 263(7), 3462-3465]. We report here the structure of Urechis hemoglobin in the cyanomet state refined to 2.5 A resolution by simulated annealing yielding R = 0.148 for reflections F greater than 3 sigma between 5.0 and 2.5 A resolution. The starting model was fitted to a map originally derived from multiple-wavelength anomalous-dispersion phases to 3 A resolution that was then subjected to cyclic twofold molecular averaging and solvent flattening. Structural analysis of the resultant model shows that the unique quaternary assemblage is possible due to several favorable interactions between subunits, including salt links, hydrophobic pockets and interactions mediated by bound water. The tetramer is stabilized by subunit-subunit interactions between the G/H turns and D helices within the crystallographic dimer, and the A/B turn regions and E helices between subunits related by a molecular twofold axis. Interestingly, each subunit has one cysteine residue (Cys21) located in the A/B turn. These twofold-related cysteinyl residues are near enough to one another to form a disulfide bridge but do not.

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Related Citations: 

• Novel Subunit Structure Observed for Noncooperative Hemoglobin from Urechis Caupo
  Kolatkar, P.R., Meador, W.E., Stanfield, R.L., Hackert, M.L.
  (1988) J Biol Chem 263: 3462

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Texas, Austin 78712.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN (CYANO MET)	A, B	141	Urechis caupo	Mutation(s): 0  Gene Names: CDNA
UniProt
Find proteins for P06148 (Urechis caupo) Explore P06148  Go to UniProtKB:  P06148

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CYN	C [auth A], E [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.147 
• R-Value Observed: 0.147 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.8	α = 90
b = 54.9	β = 90
c = 110.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1991-12-03 
• Released Date: 1993-10-31 
Deposition Author(s): Hackert, M., Kolatkar, P., Ernst, S.R., Ogata, C.M., Hendrickson, W.A., Merritt, E.A., Phizackerley, R.P.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance