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PDBsum entry 1sdk
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protein ligands Protein-protein interface(s) links
Oxygen transport PDB id
1sdk

 

 

 

 

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Contents
Protein chains
141 a.a. *
146 a.a. *
Ligands
HEM-CMO ×4
TMM
Waters ×439
* Residue conservation analysis
PDB id:
1sdk
Name: Oxygen transport
Title: Cross-linked, carbonmonoxy hemoglobin a
Structure: Hemoglobin a. Chain: a, c. Other_details: cross-linked, carbonmonoxy. Hemoglobin a. Chain: b, d. Other_details: cross-linked, carbonmonoxy
Source: Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.139    
Authors: M.A.Schumacher,M.M.Dixon,R.Kluger,R.T.Jones,R.G.Brennan
Key ref: M.A.Schumacher et al. (1995). Allosteric transition intermediates modelled by crosslinked haemoglobins. Nature, 375, 84-87. PubMed id: 7723849
Date:
26-Feb-96     Release date:   01-Aug-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P69905  (HBA_HUMAN) -  Hemoglobin subunit alpha from Homo sapiens
Seq:
Struc: 		142 a.a.
141 a.a.
Protein chains
Pfam   ArchSchema ?
P68871  (HBB_HUMAN) -  Hemoglobin subunit beta from Homo sapiens
Seq:
Struc: 		147 a.a.
146 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Nature 375:84-87 (1995)
PubMed id: 7723849  
 
 
Allosteric transition intermediates modelled by crosslinked haemoglobins.
M.A.Schumacher, M.M.Dixon, R.Kluger, R.T.Jones, R.G.Brennan.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19217393 A.N.Kirschner, J.Sorem, R.Longnecker, and T.S.Jardetzky (2009).
Structure of Epstein-Barr virus glycoprotein 42 suggests a mechanism for triggering receptor-activated virus entry.
  Structure, 17, 223-233.
PDB code: 3fd4
18442134 D.J.Cipriano, and S.D.Dunn (2008).
Tethering polypeptides through bifunctional PEG cross-linking agents to probe protein function: application to ATP synthase.
  Proteins, 73, 458-467.  
17279499 M.Saito, and I.Okazaki (2007).
A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: dynamics of tertiary and quaternary structures.
  J Comput Chem, 28, 1129-1136.  
12093902 A.Riccio, L.Vitagliano, G.di Prisco, A.Zagari, and L.Mazzarella (2002).
The crystal structure of a tetrameric hemoglobin in a partial hemichrome state.
  Proc Natl Acad Sci U S A, 99, 9801-9806.
PDB code: 1la6
12023247 L.Mouawad, D.Perahia, C.H.Robert, and C.Guilbert (2002).
New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations.
  Biophys J, 82, 3224-3245.  
11369847 M.K.Safo, and D.J.Abraham (2001).
The X-ray structure determination of bovine carbonmonoxy hemoglobin at 2.1 A resoultion and its relationship to the quaternary structures of other hemoglobin crystal froms.
  Protein Sci, 10, 1091-1099.
PDB code: 1fsx
10737937 H.E.Kwansa, A.D.Young, D.Arosio, A.Razynska, and E.Bucci (2000).
Adipyl crosslinked bovine hemoglobins as new models of allosteric systems.
  Proteins, 39, 166-169.  
11112521 T.C.Mueser, P.H.Rogers, and A.Arnone (2000).
Interface sliding as illustrated by the multiple quaternary structures of liganded hemoglobin.
  Biochemistry, 39, 15353-15364.
PDB codes: 1g08 1g09 1g0a 1g0b
10194373 J.Huang, L.J.Juszczak, E.S.Peterson, C.F.Shannon, M.Yang, S.Huang, G.V.Vidugiris, and J.M.Friedman (1999).
The conformational and dynamic basis for ligand binding reactivity in hemoglobin Ypsilanti (beta 99 asp-->Tyr): origin of the quaternary enhancement effect.
  Biochemistry, 38, 4514-4525.  
10500299 J.R.Tame (1999).
What is the true structure of liganded haemoglobin?
  Trends Biochem Sci, 24, 372-377.  
9591687 E.Bucci, Z.Gryczynski, A.Razynska, and H.Kwansa (1998).
Entropy-driven intermediate steps of oxygenation may regulate the allosteric behavior of hemoglobin.
  Biophys J, 74, 2638-2648.  
9826627 M.B.Johnson, J.G.Adamson, and A.G.Mauk (1998).
Functional comparison of specifically cross-linked hemoglobins biased toward the R and T states.
  Biophys J, 75, 3078-3084.  
9646860 M.F.Perutz, A.J.Wilkinson, M.Paoli, and G.G.Dodson (1998).
The stereochemical mechanism of the cooperative effects in hemoglobin revisited.
  Annu Rev Biophys Biomol Struct, 27, 1.  
9517546 X.Ji, M.Braxenthaler, J.Moult, C.Fronticelli, E.Bucci, and G.L.Gilliland (1998).
Conformation of the sebacyl beta1Lys82-beta2Lys82 crosslink in T-state human hemoglobin.
  Proteins, 30, 309-320.  
9223339 A.Watty, C.Methfessel, and F.Hucho (1997).
Fixation of allosteric states of the nicotinic acetylcholine receptor by chemical cross-linking.
  Proc Natl Acad Sci U S A, 94, 8202-8207.  
9440206 K.D.Vandegriff, M.McCarthy, R.J.Rohlfs, and R.M.Winslow (1997).
Colloid osmotic properties of modified hemoglobins: chemically cross-linked versus polyethylene glycol surface-conjugated.
  Biophys Chem, 69, 23-30.  
9223274 M.A.Schumacher, E.E.Zheleznova, K.S.Poundstone, R.Kluger, R.T.Jones, and R.G.Brennan (1997).
Allosteric intermediates indicate R2 is the liganded hemoglobin end state.
  Proc Natl Acad Sci U S A, 94, 7841-7844.
PDB codes: 1hab 1hac
8994883 A.Mattevi, M.Rizzi, and M.Bolognesi (1996).
New structures of allosteric proteins revealing remarkable conformational changes.
  Curr Opin Struct Biol, 6, 824-829.  
8639491 E.Bucci, A.Razynska, H.Kwansa, Z.Gryczynski, J.H.Collins, C.Fronticelli, R.Unger, M.Braxenthaler, J.Moult, X.Ji, and G.Gilliland (1996).
Positive and negative cooperativities at subsequent steps of oxygenation regulate the allosteric behavior of multistate sebacylhemoglobin.
  Biochemistry, 35, 3418-3425.
PDB code: 1cls
  8756640 G.Büküşoğlu, and D.D.Jenness (1996).
Agonist-specific conformational changes in the yeast alpha-factor pheromone receptor.
  Mol Cell Biol, 16, 4818-4823.  
8557672 R.T.Jones, D.T.Shih, T.S.Fujita, Y.Song, H.Xiao, C.Head, and R.Kluger (1996).
A doubly cross-linked human hemoglobin. Effects of cross-links between different subunits.
  J Biol Chem, 271, 675-680.  
7584998 R.M.Winslow (1995).
Blood substitutes--a moving target.
  Nat Med, 1, 1212-1215.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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