5KER

Deer mouse recombinant hemoglobin from high altitude species

• PDB DOI: https://doi.org/10.2210/pdb5KER/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Peromyscus maniculatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-10 Released: 2017-04-05 
• Deposition Author(s): Inoguchi, N., Natarajan, C., Storz, J.F., Moriyama, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.202 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Alteration of the alpha 1 beta 2/ alpha 2 beta 1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice.

Inoguchi, N., Mizuno, N., Baba, S., Kumasaka, T., Natarajan, C., Storz, J.F., Moriyama, H.

(2017) PLoS One 12: e0174921-e0174921

• PubMed: 28362841 
• DOI: https://doi.org/10.1371/journal.pone.0174921
• Primary Citation of Related Structures:  
  5KER


• PubMed Abstract: 
  

  Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant.

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Organizational Affiliation: 

School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America.

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 (software)

Biological Assembly 2  

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 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.65 kDa 
• Atom Count: 9,639 
• Modelled Residue Count: 1,144 
• Deposited Residue Count: 1,148 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-globin	A [auth C], C [auth E], E [auth G], G [auth A]	141	Peromyscus maniculatus	Mutation(s): 0  Gene Names: HBA, Hba, HBAT1
UniProt
Find proteins for A4ZQ87 (Peromyscus maniculatus) Explore A4ZQ87  Go to UniProtKB:  A4ZQ87

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta globin	B [auth D], D [auth F], F [auth H], H [auth B]	146	Peromyscus maniculatus	Mutation(s): 0  Gene Names: HBB, HBB-T1, HBB-T2
UniProt
Find proteins for B7SBL4 (Peromyscus maniculatus) Explore B7SBL4  Go to UniProtKB:  B7SBL4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.202 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.182	α = 90
b = 229.618	β = 119.12
c = 53.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Inoguchi, N., Natarajan, C., Storz, J.F., Moriyama, H.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2017-04-19
  Changes: Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description