6IHX

Crystal Structure Analysis of bovine Hemoglobin modified by SNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

This is version 1.2 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: https://doi.org/10.1021/acs.jpcb.8b10077
  • Primary Citation of Related Structures:  
    6IHX, 6II1

  • PubMed Abstract: 

    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

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
140Bos taurusMutation(s): 0 
UniProt
Find proteins for P01966 (Bos taurus)
Explore P01966 
Go to UniProtKB:  P01966
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01966
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
B, D
144Bos taurusMutation(s): 0 
UniProt
Find proteins for P02070 (Bos taurus)
Explore P02070 
Go to UniProtKB:  P02070
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02070
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CMO
Query on CMO

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.117α = 90
b = 78.132β = 90
c = 109.539γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description