3HYU | pdb_00003hyu

Crystal structure of the altitude adapted hemoglobin of guinea pig.

• PDB DOI: https://doi.org/10.2210/pdb3HYU/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Cavia porcellus
• Mutation(s): No 


• Deposited: 2009-06-23 Released: 2010-06-23 
• Deposition Author(s): Pairet, B., Jaenicke, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structure of the altitude adapted hemoglobin of guinea pig in the R2-state.

Pairet, B., Jaenicke, E.

(2010) PLoS One 5: e12389-e12389

• PubMed: 20811494 
• DOI: https://doi.org/10.1371/journal.pone.0012389
• Primary Citation of Related Structures:  
  3HYU


• PubMed Abstract: 
  

  Guinea pigs are considered to be genetically adapted to a high altitude environment based on the consistent finding of a high oxygen affinity of their blood. The crystal structure of guinea pig hemoglobin at 1.8 A resolution suggests that the increased oxygen affinity of guinea pig hemoglobin can be explained by two factors, namely a decreased stability of the T-state and an increased stability of the R2-state. The destabilization of the T-state can be related to the substitution of a highly conserved proline (P44) to histidine (H44) in the alpha-subunit, which causes a steric hindrance with H97 of the beta-subunit in the switch region. The stabilization of the R2-state is caused by two additional salt bridges at the beta1/beta2 interface. Both factors together are supposed to serve to shift the equilibrium between the conformational states towards the high affinity relaxed states resulting in an increased oxygen affinity.

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Organizational Affiliation: 
• Institut für Molekulare Biophysik, Johannes Gutenberg Universität, Mainz, Germany.

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.

Macromolecule Content 

• Total Structure Weight: 32.81 kDa 
• Atom Count: 2,537 
• Modeled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	141	Cavia porcellus	Mutation(s): 0
UniProt
Find proteins for P01947 (Cavia porcellus) Explore P01947  Go to UniProtKB:  P01947

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Cavia porcellus	Mutation(s): 0
UniProt
Find proteins for P02095 (Cavia porcellus) Explore P02095  Go to UniProtKB:  P02095

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
PO4	D [auth A], F [auth B], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.54	α = 90
b = 89.95	β = 90
c = 82.72	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Pairet, B., Jaenicke, E.

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-28
  Changes: Database references
• Version 1.3: 2015-02-18
  Changes: Other
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description