6II1

Crystal Structure Analysis of CO form hemoglobin from Bos taurus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Quaternary Structure Analysis of a Hemoglobin Core in Hemoglobin-Albumin Cluster.

Morita, Y.Yamada, T.Kureishi, M.Kihira, K.Komatsu, T.

(2018) J Phys Chem B 122: 12031-12039

  • DOI: 10.1021/acs.jpcb.8b10077
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A core-shell ensemble of bovine hemoglobin (Hb) and human serum albumin (HSA) is an artificial O <sub>2 </sub> carrier as a red blood cell substitute. This protein particle is created by covalent wrapping of a carbonyl Hb with HSAs: Hb <sup>R </sup>- ...

    A core-shell ensemble of bovine hemoglobin (Hb) and human serum albumin (HSA) is an artificial O 2 carrier as a red blood cell substitute. This protein particle is created by covalent wrapping of a carbonyl Hb with HSAs: Hb R -HSA 3 cluster, where Hb R signifies the use of carbonyl Hb (relaxed (R) state conformation) as a starting material. The Hb R -HSA 3 cluster exhibits high O 2 affinity and low cooperativity. Analysis of the quaternary structure of the central Hb R in the cluster revealed that its high O 2 affinity is attributed to the physically immobile Hb R nucleus. Circular dichroism and UV-vis absorption spectroscopy showed that the structure of deoxy Hb R core closely resembles the R-state. The crystal structure of Lys-modified carbonyl Hb R was superimposed on that of carbonyl Hb. These results imply that chemical modifications of the surface Lys groups and Cys-93(β) of the carbonyl Hb with cross-linking agent interfered in the quaternary structure movement from the R-state to tense (T) state. As expected, coupling of deoxy Hb (T-state) with HSAs yielded Hb T -HSA 3 cluster having low O 2 affinity. The mixing of Hb R -HSA 3 and Hb T -HSA 3 clusters conferred a tailor-made formulation of artificial O 2 carrier with a desired O 2 affinity ( P 50 ).


    Organizational Affiliation

    JEM Utilization Center, Human Spaceflight Technology Directorate , Japan Aerospace Exploration Agency (JAXA) , 2-1-1 Sengen , Tsukuba-shi , Ibaraki 305-8505 , Japan.,Department of Applied Chemistry, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A, C
138Bos taurusMutation(s): 0 
Gene Names: HBA
Find proteins for P01966 (Bos taurus)
Go to UniProtKB:  P01966
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B, D
145Bos taurusMutation(s): 0 
Gene Names: HBB
Find proteins for P02070 (Bos taurus)
Go to Gene View: HBB
Go to UniProtKB:  P02070
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B, C, D
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.560α = 90.00
b = 76.283β = 90.00
c = 109.789γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references