1CLS

CROSS-LINKED HUMAN HEMOGLOBIN DEOXY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Positive and negative cooperativities at subsequent steps of oxygenation regulate the allosteric behavior of multistate sebacylhemoglobin.

Bucci, E.Razynska, A.Kwansa, H.Gryczynski, Z.Collins, J.H.Fronticelli, C.Unger, R.Braxenthaler, M.Moult, J.Ji, X.Gilliland, G.

(1996) Biochemistry 35: 3418-3425

  • DOI: 10.1021/bi952446b

  • PubMed Abstract: 
  • Cross-linked human hemoglobin (HbA) is obtained by reaction with bis(3,5-dibromosalicyl) sebacate. Peptide maps and crystallographic analyses confirm the presence of the 10 carbon atom long sebacyl residue cross-linking the two beta82 lysines of the ...

    Cross-linked human hemoglobin (HbA) is obtained by reaction with bis(3,5-dibromosalicyl) sebacate. Peptide maps and crystallographic analyses confirm the presence of the 10 carbon atom long sebacyl residue cross-linking the two beta82 lysines of the beta-cleft (DecHb). The Adair's constants, obtained from the oxygen binding isotherms, show that at the first step of oxygenation normal hemoglobin and DecHb have a very similar oxygen affinity. In DecHb negative binding cooperativity is present at the second step of oxygenation, which has an affinity 27 times lower than at the first step. Positive cooperativity is present at the third binding step, whose affinity is 380 times that of the second step. The fourth binding step shows a weak negative cooperativity with an affinity one-half that of the third step. Crystals of deoxy-DecHb diffracted to 1.9 angstroms resolution. The resulting atomic coordinates are very similar to those of Fermi et al. [(1984) J. Mol.Biol. 175, 159-174] and Fronticelli et al. [(1994) J. Biol Chem. 269, 23965-23969] for deoxy-HbA. The electron density map of deoxy-DecHb indicates the presence of the 10 carbon bridge between the beta82 lysines. Molecular modeling confirms that insertion of the linker into the T structure requires only slight displacement of the two beta82 lysines. Instead, insertion of the linker into the R and R2 structures [Shaanan (1983) J. Mol. Biol. 171, 31-59; Silva et al. (1992) J. Biol. Chem. 267, 17248-17256] is hindered by serious sterical restrictions. The linker primarily affects the partially and fully liganded states of hemoglobin. The data suggest in DecHb concerted conformational changes at each step of oxygenation.


    Related Citations: 
    • Chloride Ion Independence of the Bohr Effect in a Mutant Human Hemoglobin Beta (V1M+H2Deleted)
      Fronticelli, C.,Pechik, I.,Brinigar, W.S.,Kowalczyk, J.,Gilliland, G.L.
      (1994) J.Biol.Chem. 269: 23965


    Organizational Affiliation

    Department of Biological Chemistry, University of Maryland School of Medicine, Baltimore 21201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN
A, C
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN
B, D
146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
O
Query on O

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Download CCD File 
A, C
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

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Download CCD File 
D
SEBACIC ACID
C10 H18 O4
CXMXRPHRNRROMY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.800α = 90.00
b = 82.470β = 99.24
c = 53.300γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
GPRLSArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance