1NEJ | pdb_00001nej

Crystalline Human Carbonmonoxy Hemoglobin S (Liganded Sickle Cell Hemoglobin) Exhibits The R2 Quaternary State At Neutral pH In The Presence Of Polyethylene Glycol: The 2.1 Angstrom Resolution Crystal Structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.268 (Depositor) 
  • R-Value Work: 
    0.235 (Depositor), 0.286 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

COHbC and COHbS crystallize in the R2 quaternary state at neutral pH in the presence of PEG 4000.

Patskovska, L.N.Patskovsky, Y.V.Almo, S.C.Hirsch, R.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 566-573

  • DOI: https://doi.org/10.1107/S0907444905004622
  • Primary Citation Related Structures: 
    1M9P, 1NEJ

  • PubMed Abstract: 

    Human hemoglobin binds oxygen cooperatively and functions as a tetramer composed of two identical alphabeta heterodimers. While human hemoglobin is the best characterized allosteric protein, the quaternary R (oxygenated or liganded) to T (deoxygenated) structural transition remains controversial. The R2 state has been postulated to represent either an intermediate or final quaternary state elicited by ligand binding. However, the biological relevance of the R2 state has been questioned as it has not been observed crystallographically under physiological conditions. The high-resolution R2 quaternary structures of human COHbC (betaE6K) and COHbS (betaE6V) are reported at neutral pH and low ionic strength using PEG 4000 as a precipitant. Crystals of COHbC, COHbS and their mixtures are isomorphous, indicating that they share the same tertiary and quaternary structures. In contrast, oxyHbA or COHbA did not yield crystals at neutral pH under similar conditions. Solubility studies and modeling suggest that at neutral pH and low ionic strength the beta6 mutant hemoglobins crystallize (betaK6 > betaV6) as a result of more favorable lattice contacts.


  • Organizational Affiliation
    • Department of Medicine (Division of Hematology), Albert Einstein College of Medicine, Bronx, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 64.6 kDa 
  • Atom Count: 4,793 
  • Modeled Residue Count: 574 
  • Deposited Residue Count: 574 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin alpha chain
A, C
141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin beta chain
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 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: 2.10 Å
  • R-Value Free:  0.268 (Depositor) 
  • R-Value Work:  0.235 (Depositor), 0.286 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58α = 90
b = 58.53β = 90
c = 171.84γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description