1SDL

CROSS-LINKED, CARBONMONOXY HEMOGLOBIN A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Allosteric transition intermediates modelled by crosslinked haemoglobins.

Schumacher, M.A.Dixon, M.M.Kluger, R.Jones, R.T.Brennan, R.G.

(1995) Nature 375: 84-87

  • DOI: https://doi.org/10.1038/375084a0
  • Primary Citation of Related Structures:  
    1SDK, 1SDL

  • PubMed Abstract: 

    The structural end-points of haemoglobin's transition from its low-oxygen-affinity (T) to high-oxygen-affinity (R) state, have been well established by X-ray crystallography, but short-lived intermediates have proved less amenable to X-ray studies. Here we use chemical crosslinking to fix these intermediates for structural characterization. We describe the X-ray structures of three haemoglobins, alpha 2 beta 1S82 beta, alpha 2 beta 1Tm82 beta and alpha 2 beta 1,82Tm82 beta, which were crosslinked between the amino groups of residues beta Val1 and beta Lys82 by 3,3'-stilbenedicarboxylic acid (S) or trimesic acid (Tm) while in the deoxy state, and saturated with carbon monoxide before crystallization. alpha 2 beta 1S82 beta, which has almost normal oxygen affinity, is completely in the R-state conformation; however, alpha 2 beta 1Tm82 beta and alpha 2 beta 1,82Tm82 beta, both of which have low oxygen affinity, have been prevented from completing their transition into the R state and display many features of a transitional intermediate. These haemoglobins therefore represent a snapshot of the nascent R state.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMOGLOBIN A
A, C
141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HEMOGLOBIN A
B, D
146Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 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
TMM
Query on TMM

Download Ideal Coordinates CCD File 
M [auth D]1,3,5-BENZENETRICARBOXYLIC ACID
C9 H6 O6
QMKYBPDZANOJGF-UHFFFAOYSA-N
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: 1.80 Å
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.43α = 90
b = 72.16β = 108.25
c = 88.03γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-08-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other