6KYE

The crystal structure of recombinant human adult hemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Genetically engineered haemoglobin wrapped covalently with human serum albumins as an artificial O2carrier.

Funaki, R.Okamoto, W.Endo, C.Morita, Y.Kihira, K.Komatsu, T.

(2020) J Mater Chem B 8: 1139-1145

  • DOI: 10.1039/c9tb02184a
  • Primary Citation of Related Structures:  
    6KYE

  • PubMed Abstract: 
  • We describe the synthesis and O 2 affinity of genetically engineered human adult haemoglobin (rHbA) wrapped covalently with recombinant human serum albumins (rHSAs) as an artificial O 2 carrier used for a completely synthetic red blood cell (RBC) substitute ...

    We describe the synthesis and O 2 affinity of genetically engineered human adult haemoglobin (rHbA) wrapped covalently with recombinant human serum albumins (rHSAs) as an artificial O 2 carrier used for a completely synthetic red blood cell (RBC) substitute. Wild-type rHbA [rHbA(wt)] expressed in yeast species Pichia pastoris shows an identical amino acid sequence and three-dimensional structure to those of native HbA. It is particularly interesting that two orientations of the prosthetic haem group in rHbA(wt) were aligned by gentle heating in the natural form. Covalent wrapping of rHbA(wt) with three rHSAs conferred a core-shell structured haemoglobin-albumin cluster: rHbA(wt)-rHSA 3 . Three variant clusters containing an rHbA mutant core were also created: Leu-β28 → Phe, Leu-β28 → Trp, and Leu-β28 → Tyr/His-β63 → Gln. Replacement of Leu-β28 with Trp decreased the distal space in the haem pocket, thereby yielding a cluster with moderately low O 2 affinity which is nearly the same as that of human RBC.


    Organizational Affiliation

    Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan. komatsu@kc.chuo-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit alphaA, C, E, G, I, K142Homo sapiensMutation(s): 0 
Gene Names: HBA1HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit betaB, D, F, H, J, L147Homo sapiensMutation(s): 0 
Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth H] , CA [auth I] , EA [auth J] , GA [auth K] , IA [auth L] , M [auth A] , O [auth B] , Q [auth C] , 
AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
BA [auth H] , DA [auth I] , FA [auth J] , HA [auth K] , JA [auth L] , N [auth A] , P [auth B] , R [auth C] , 
BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.031α = 90
b = 55.947β = 98.27
c = 133.156γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan18K19007

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references