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PDBsum entry 1a3n
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protein ligands Protein-protein interface(s) links
Oxygen transport PDB id
1a3n

 

 

 

 

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Contents
Protein chains
141 a.a. *
145 a.a. *
Ligands
HEM ×4
Waters ×455
* Residue conservation analysis
PDB id:
1a3n
Name: Oxygen transport
Title: Deoxy human hemoglobin
Structure: Hemoglobin (alpha chain). Chain: a, c. Hemoglobin (beta chain). Chain: b, d
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Cell: red cell. Cell: red cell
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.171     R-free:   0.220
Authors: J.Tame,B.Vallone
Key ref:
J.R.Tame and B.Vallone (2000). The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K. Acta Crystallogr D Biol Crystallogr, 56, 805-811. PubMed id: 10930827 DOI: 10.1107/S0907444900006387
Date:
22-Jan-98     Release date:   29-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 

 
DOI no: 10.1107/S0907444900006387 Acta Crystallogr D Biol Crystallogr 56:805-811 (2000)
PubMed id: 10930827  
 
 
The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K.
J.R.Tame, B.Vallone.
 
  ABSTRACT  
 
The structures of deoxy human haemoglobin and an artificial mutant (Tyralpha42-->His) have been solved at 120 K. While overall agreement between these structures and others in the PDB is very good, certain side chains are found to be shifted, absent from the electron-density map or in different rotamers. Non-crystallographic symmetry (NCS) is very well obeyed in the native protein, but not around the site of the changed residue in the mutant. NCS is also not obeyed by the water molecule invariably found in the alpha-chain haem pocket in room-temperature crystal structures of haemoglobin. At 120 K, this water molecule disappears from one alpha chain in the asymmetric unit but not the other.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 The [1] haem. The 2F[o] - F[c] electron-density map is contoured at 1 . 		Figure 3.
Figure 3 His [1]42. The 2F[o] - F[c] electron-density map shows the residues neighbouring [1]42 are undisturbed by the mutation from tyrosine.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 805-811) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21415366 S.Fischer, K.W.Olsen, K.Nam, and M.Karplus (2011).
Unsuspected pathway of the allosteric transition in hemoglobin.
  Proc Natl Acad Sci U S A, 108, 5608-5613.  
20823548 E.Pozharski (2010).
Percentile-based spread: a more accurate way to compare crystallographic models.
  Acta Crystallogr D Biol Crystallogr, 66, 970-978.  
19365817 C.Savino, A.E.Miele, F.Draghi, K.A.Johnson, G.Sciara, M.Brunori, and B.Vallone (2009).
Pattern of cavities in globins: The case of human hemoglobin.
  Biopolymers, 91, 1097-1107.
PDB codes: 2w6v 2w6w 2w72
18676657 N.Kantarci-Carsibasi, T.Haliloglu, and P.Doruker (2008).
Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.
  Biophys J, 95, 5862-5873.  
17208980 C.Bertonati, B.Honig, and E.Alexov (2007).
Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies.
  Biophys J, 92, 1891-1899.  
17598909 D.Tobi, and I.Bahar (2007).
Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity?
  BMC Bioinformatics, 8, 226.  
17691822 S.C.Sahu, V.Simplaceanu, Q.Gong, N.T.Ho, F.Tian, J.H.Prestegard, and C.Ho (2007).
Insights into the solution structure of human deoxyhemoglobin in the absence and presence of an allosteric effector.
  Biochemistry, 46, 9973-9980.  
17497935 X.J.Song, Y.Yuan, V.Simplaceanu, S.C.Sahu, N.T.Ho, and C.Ho (2007).
A comparative NMR study of the polypeptide backbone dynamics of hemoglobin in the deoxy and carbonmonoxy forms.
  Biochemistry, 46, 6795-6803.  
15495251 O.Abdulmalik, M.K.Safo, N.B.Lerner, J.Ochotorena, E.Daikhin, V.Lakka, R.Santacroce, D.J.Abraham, and T.Asakura (2004).
Characterization of hemoglobin bassett (alpha94Asp-->Ala), a variant with very low oxygen affinity.
  Am J Hematol, 77, 268-276.
PDB codes: 1r1x 1r1y
15117955 T.Yokoyama, K.T.Chong, G.Miyazaki, H.Morimoto, D.T.Shih, S.Unzai, J.R.Tame, and S.Y.Park (2004).
Novel mechanisms of pH sensitivity in tuna hemoglobin: a structural explanation of the root effect.
  J Biol Chem, 279, 28632-28640.
PDB codes: 1v4u 1v4w 1v4x
12417758 P.J.Bickel, K.J.Kechris, P.C.Spector, G.J.Wedemayer, and A.N.Glazer (2002).
Inaugural Article: finding important sites in protein sequences.
  Proc Natl Acad Sci U S A, 99, 14764-14771.  
11296285 N.E.Robinson, and A.B.Robinson (2001).
Prediction of protein deamidation rates from primary and three-dimensional structure.
  Proc Natl Acad Sci U S A, 98, 4367-4372.  
11747613 T.Chen, J.D.Jaffe, and G.M.Church (2001).
Algorithms for identifying protein cross-links via tandem mass spectrometry.
  J Comput Biol, 8, 571-583.  
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 codes are shown on the right.

 

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