1SPG | pdb_00001spg

CARBONMONOXY HEMOGLOBIN FROM THE TELEOST FISH LEIOSTOMUS XANTHURUS

• PDB DOI: https://doi.org/10.2210/pdb1SPG/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Leiostomus xanthurus
• Mutation(s): No 


• Deposited: 1996-02-05 Released: 1997-03-12 
• Deposition Author(s): Mylvaganam, S.E., Getzoff, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.245 (Depositor) 
• R-Value Work: 
  0.191 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Structural basis for the root effect in haemoglobin.

Mylvaganam, S.E., Bonaventura, C., Bonaventura, J., Getzoff, E.D.

(1996) Nat Struct Biol 3: 275-283

• PubMed: 8605630 
• DOI: https://doi.org/10.1038/nsb0396-275
• Primary Citation Related Structures: 
  1SPG


• PubMed Abstract: 
  

  The remarkable ability of root effect haemoglobins to pump oxygen against high O2 gradients results from extreme, acid-induced reductions in O2 affinity and cooperativity. The long-sought mechanism for the root effect, revealed by the 2 angstrom crystal structure of the ligand-bound haemoglobin from Leiostomus xanthurus at pH 7.5, unexpectedly involves modulation of the R-state. Key residues strategically assemble positive-charge clusters across the allosteric beta1 beta2-interface in the R-state. At low pH, protonation of the beta N terminus and His 147(HC3)beta within these clusters is postulated to destabilize the R-state and promote the acid-triggered, allosteric R-->T switch with concomitant O2 release. Surprisingly, a set of residues specific to root effect haemoglobins recruit additional residues, conserved among most haemoglobins, to produce the root effect.

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Organizational Affiliation: 
• The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.29 kDa 
• Atom Count: 2,518 
• Modeled Residue Count: 291 
• Deposited Residue Count: 291 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN	A	144	Leiostomus xanthurus	Mutation(s): 0
UniProt
Find proteins for P56250 (Leiostomus xanthurus) Explore P56250  Go to UniProtKB:  P56250

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOGLOBIN	B	147	Leiostomus xanthurus	Mutation(s): 0
UniProt
Find proteins for P56251 (Leiostomus xanthurus) Explore P56251  Go to UniProtKB:  P56251

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.245 (Depositor) 
• R-Value Work:  0.191 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.6	α = 90
b = 75.6	β = 141.9
c = 69.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-03-12 
Deposition Author(s): Mylvaganam, S.E., Getzoff, E.D.

Revision History  

• Version 1.0: 1997-03-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-16
  Changes: Structure summary