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PDBsum entry 1j3y
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protein ligands Protein-protein interface(s) links
Oxygen storage/transport PDB id
1j3y

 

 

 

 

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Contents
Protein chains
141 a.a. *
146 a.a. *
Ligands
HEM ×4
CMO ×4
HNI ×4
2FU ×2
Waters ×2272
* Residue conservation analysis
PDB id:
1j3y
Name: Oxygen storage/transport
Title: Direct observation of photolysis-induced tertiary structural changes in human hemoglobin; crystal structure of alpha(fe)-beta(ni) hemoglobin (laser photolysed)
Structure: Hemoglobin alpha chain. Chain: a, c, e, g. Hemoglobin beta chain. Chain: b, d, f, h
Source: Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606
Biol. unit: Tetramer (from PQS)
Resolution:
1.55Å     R-factor:   0.164     R-free:   0.205
Authors: S.Adachi,S.-Y.Park,J.R.H.Tame,Y.Shiro,N.Shibayama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
S.Adachi et al. (2003). Direct observation of photolysis-induced tertiary structural changes in hemoglobin. Proc Natl Acad Sci U S A, 100, 7039-7044. PubMed id: 12773618 DOI: 10.1073/pnas.1230629100
Date:
21-Feb-03     Release date:   22-Jul-03    
PROCHECK
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 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

 

 
DOI no: 10.1073/pnas.1230629100 Proc Natl Acad Sci U S A 100:7039-7044 (2003)
PubMed id: 12773618  
 
 
Direct observation of photolysis-induced tertiary structural changes in hemoglobin.
S.Adachi, S.Y.Park, J.R.Tame, Y.Shiro, N.Shibayama.
 
  ABSTRACT  
 
Human Hb, an alpha2beta2 tetrameric oxygen transport protein that switches from a T (tense) to an R (relaxed) quaternary structure during oxygenation, has long served as a model for studying protein allostery in general. Time-resolved spectroscopic measurements after photodissociation of CO-liganded Hb have played a central role in exploring both protein dynamical responses and molecular cooperativity, but the direct visualization and the structural consequences of photodeligation have not yet been reported. Here we present an x-ray study of structural changes induced by photodissociation of half-liganded T-state and fully liganded R-state human Hb at cryogenic temperatures (25-35 K). On photodissociation of CO, structural changes involving the heme and the F-helix are more marked in the alpha subunit than in the beta subunit, and more subtle in the R state than in the T state. Photodeligation causes a significant sliding motion of the T-state beta heme. Our results establish that the structural basis of the low affinity of the T state is radically different between the subunits, because of differences in the packing and chemical tension at the hemes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereoview of electron density maps (2F[o] - F[c] map) of the active-site structures of photolysed CO complexes of T-state hybrid Hbs contoured at 1.3 . (a) The 1 heme region in photolysed XL[ (Fe-CO) (Ni)][2] (molecule 1) at 25 K. (b) The 2 heme region in photolysed XL[ (Ni) (Fe-CO)][2] (molecule 2) at 25 K. 		Figure 3.
Fig. 3. Stereoview of difference Fourier maps of the active-site structures between the R-state photoproduct and the CO-bound structure contoured at ±3 . (a) The heme region in HbCO at 35 K. (b) The heme region in HbCO at 35 K.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20164645 A.Tomita, T.Sato, S.Nozawa, S.Y.Koshihara, and S.Adachi (2010).
Tracking ligand-migration pathways of carbonmonoxy myoglobin in crystals at cryogenic temperatures.
  Acta Crystallogr A, 66, 220-228.  
20179337 T.Kuwada, T.Hasegawa, T.Takagi, I.Sato, and F.Shishikura (2010).
pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera).
  Acta Crystallogr D Biol Crystallogr, 66, 258-267.
PDB codes: 2zwj 3a5a 3a5b 3a5g 3a9m
19204297 A.Tomita, T.Sato, K.Ichiyanagi, S.Nozawa, H.Ichikawa, M.Chollet, F.Kawai, S.Y.Park, T.Tsuduki, T.Yamato, S.Y.Koshihara, and S.Adachi (2009).
Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin.
  Proc Natl Acad Sci U S A, 106, 2612-2616.
PDB codes: 2zsn 2zso 2zsp 2zsq 2zsr 2zss 2zst 2zsx 2zsy 2zsz 2zt0 2zt1 2zt2 2zt3 2zt4 3e4n 3e55 3e5i 3e5o 3ecl 3ecx 3ecz 3ed9 3eda 3edb
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
18380000 C.Ciaccio, A.Coletta, G.De Sanctis, S.Marini, and M.Coletta (2008).
Cooperativity and allostery in haemoglobin function.
  IUBMB Life, 60, 112-123.  
18096633 M.Laberge, and T.Yonetani (2008).
Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics.
  Biophys J, 94, 2737-2751.  
17335583 C.H.Tung, J.W.Huang, and J.M.Yang (2007).
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
  Genome Biol, 8, R31.  
18003918 R.E.Alcantara, C.Xu, T.G.Spiro, and V.Guallar (2007).
A quantum-chemical picture of hemoglobin affinity.
  Proc Natl Acad Sci U S A, 104, 18451-18455.  
16684887 J.E.Knapp, R.Pahl, V.Srajer, and W.E.Royer (2006).
Allosteric action in real time: time-resolved crystallographic studies of a cooperative dimeric hemoglobin.
  Proc Natl Acad Sci U S A, 103, 7649-7654.
PDB codes: 2grf 2grh 2grz
16129597 D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.
  Curr Opin Struct Biol, 15, 538-547.  
16204001 N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, and K.Miki (2005).
Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
  Proc Natl Acad Sci U S A, 102, 14521-14526.
PDB codes: 2d2m 2d2n
15300829 S.J.Kwon, R.Petri, A.L.DeBoer, and C.Schmidt-Dannert (2004).
A high-throughput screen for porphyrin metal chelatases: application to the directed evolution of ferrochelatases for metalloporphyrin biosynthesis.
  Chembiochem, 5, 1069-1074.  
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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