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

 

 

 

 

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Contents
Protein chains
146 a.a. *
Ligands
SO4 ×4
HEM-CMO ×4
Waters ×133
* Residue conservation analysis
PDB id:
1cbm
Name: Oxygen transport
Title: The 1.8 angstrom structure of carbonmonoxy-beta4 hemoglobin: analysis of a homotetramer with the r quaternary structure of liganded alpha2beta2 hemoglobin
Structure: Hemoglobin beta 4 (carbonmonoxy). Chain: a, b, c, d. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Tetramer (from PQS)
Resolution:
1.74Å     R-factor:   0.177    
Authors: G.E.O.Borgstahl,A.Arnone
Key ref: G.E.Borgstahl et al. (1994). The 1.8 A structure of carbonmonoxy-beta 4 hemoglobin. Analysis of a homotetramer with the R quaternary structure of liganded alpha 2 beta 2 hemoglobin. J Mol Biol, 236, 817-830. PubMed id: 8114096
Date:
18-Feb-93     Release date:   31-Jul-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P68871  (HBB_HUMAN) -  Hemoglobin subunit beta from Homo sapiens
Seq:
Struc: 		147 a.a.
146 a.a.
Key:    Secondary structure  CATH domain

 

 
J Mol Biol 236:817-830 (1994)
PubMed id: 8114096  
 
 
The 1.8 A structure of carbonmonoxy-beta 4 hemoglobin. Analysis of a homotetramer with the R quaternary structure of liganded alpha 2 beta 2 hemoglobin.
G.E.Borgstahl, P.H.Rogers, A.Arnone.
 
  ABSTRACT  
 
The beta-chains isolated from the human hemoglobin alpha 2 beta 2 heterotetramer self-assemble to form a beta 4 homotetramer. We report the structure of the carbonmonoxy-beta 4 (CO beta 4) tetramer refined at a resolution of 1.8 A. Compared to the three known quaternary structures of human hemoglobin, the T state, the R state and the R2 state, the quaternary structure of CO beta 4 most closely resembles the R state. While the degree of structural similarity between CO beta 4 and the R state of liganded alpha 2 beta 2 is quite high, differences between the alpha and beta-chain sequences result in interesting alternative packing arrangements at the subunit interfaces of CO beta 4. In particular, Arg40 beta and Asp99 beta interact across the CO beta 4 equivalent of the alpha 1 beta 2 interface to form two symmetry-related salt bridges that have no counterpart in either liganded or deoxyhemoglobin. Because these salt bridges are near a 2-fold symmetry axis, steric constraints prevent their simultaneous formation, and electron density images of Arg40 beta and Asp99 beta show equally populated dual conformations for the side-chains of both residues. Relative to the liganded alpha 2 beta 2 tetramer, the Arg40 beta...Asp99 beta salt bridges introduce ionic interactions that should strengthen the CO beta 4 tetramer. The CO beta 4 equivalent of the alpha 1 alpha 2 and beta 1 beta 2 interfaces strengthens the tetramer relative to the liganded alpha 2 beta 2 tetramer by tethering both ends of the central cavity. (The entrance to the central cavity is altered so that the N termini move closer together and the C termini further apart, forming an anion binding pocket that is absent in liganded alpha 2 beta 2 hemoglobin.) In contrast, analysis of the CO beta 4 counterpart of the alpha 1 beta 1 interface indicates that this interface is weakened in the CO beta 4 tetramer. These differences in interface stability provide a structural explanation for the published observation that the alpha 2 beta 2 tetramer assembles via a stable alpha 1 beta 1 dimer intermediate, whereas assembly of the CO beta 4 tetramer is characterized more accurately by a monomer-tetramer equilibrium.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19659437 T.L.Mollan, X.Yu, M.J.Weiss, and J.S.Olson (2010).
The role of alpha-hemoglobin stabilizing protein in redox chemistry, denaturation, and hemoglobin assembly.
  Antioxid Redox Signal, 12, 219-231.  
20519321 T.Shibata, S.Nagao, H.Tai, S.Nagatomo, H.Hamada, H.Yoshikawa, A.Suzuki, and Y.Yamamoto (2010).
Characterization of the acid-alkaline transition in the individual subunits of human adult and foetal methaemoglobins.
  J Biochem, 148, 217-229.  
19397368 A.L.Asmundson, A.M.Taber, A.van der Walde, D.H.Lin, J.S.Olson, and S.J.Anthony-Cahill (2009).
Coexpression of human alpha- and circularly permuted beta-globins yields a hemoglobin with normal R state but modified T state properties.
  Biochemistry, 48, 5456-5465.  
17656582 L.R.Manning, J.E.Russell, J.C.Padovan, B.T.Chait, A.Popowicz, R.S.Manning, and J.M.Manning (2007).
Human embryonic, fetal, and adult hemoglobins have different subunit interface strengths. Correlation with lifespan in the red cell.
  Protein Sci, 16, 1641-1658.  
15220346 V.Baudin-Creuza, C.Vasseur-Godbillon, C.Pato, C.Préhu, H.Wajcman, and M.C.Marden (2004).
Transfer of human alpha- to beta-hemoglobin via its chaperone protein: evidence for a new state.
  J Biol Chem, 279, 36530-36533.  
14519115 K.Shikama, and A.Matsuoka (2003).
Human haemoglobin: a new paradigm for oxygen binding involving two types of alphabeta contacts.
  Eur J Biochem, 270, 4041-4051.  
11784314 J.Yasuda, T.Ichikawa, M.Tsuruga, A.Matsuoka, Y.Sugawara, and K.Shikama (2002).
The alpha 1 beta 1 contact of human hemoglobin plays a key role in stabilizing the bound dioxygen.
  Eur J Biochem, 269, 202-211.  
11923284 M.Mito, K.T.Chong, G.Miyazaki, S.Adachi, S.Y.Park, J.R.Tame, and H.Morimoto (2002).
Crystal structures of deoxy- and carbonmonoxyhemoglobin F1 from the hagfish Eptatretus burgeri.
  J Biol Chem, 277, 21898-21905.
PDB codes: 1it2 1it3
12095481 T.Brittain (2002).
Molecular aspects of embryonic hemoglobin function.
  Mol Aspects Med, 23, 293-342.  
11514664 R.D.Kidd, H.M.Baker, A.J.Mathews, T.Brittain, and E.N.Baker (2001).
Oligomerization and ligand binding in a homotetrameric hemoglobin: two high-resolution crystal structures of hemoglobin Bart's (gamma(4)), a marker for alpha-thalassemia.
  Protein Sci, 10, 1739-1749.
PDB codes: 1i3d 1i3e
10713517 T.H.Lu, K.Panneerselvam, Y.C.Liaw, P.Kan, and C.J.Lee (2000).
Structure determination of porcine haemoglobin.
  Acta Crystallogr D Biol Crystallogr, 56, 304-312.
PDB code: 1qpw
9535834 M.Tsuruga, A.Matsuoka, A.Hachimori, Y.Sugawara, and K.Shikama (1998).
The molecular mechanism of autoxidation for human oxyhemoglobin. Tilting of the distal histidine causes nonequivalent oxidation in the beta chain.
  J Biol Chem, 273, 8607-8615.  
9624044 S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, and T.Tsukihara (1998).
Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.
  Science, 280, 1723-1729.
PDB codes: 1oco 1ocr 1ocz 2occ
9537987 Y.Guan, M.J.Hickey, G.E.Borgstahl, R.A.Hallewell, J.R.Lepock, D.O'Connor, Y.Hsieh, H.S.Nick, D.N.Silverman, and J.A.Tainer (1998).
Crystal structure of Y34F mutant human mitochondrial manganese superoxide dismutase and the functional role of tyrosine 34.
  Biochemistry, 37, 4722-4730.
PDB codes: 1ap5 1ap6
9374481 K.Inaba, K.Wakasugi, K.Ishimori, T.Konno, M.Kataoka, and I.Morishima (1997).
Structural and functional roles of modules in hemoglobin. Substitution of module M4 in hemoglobin subunits.
  J Biol Chem, 272, 30054-30060.  
9468623 K.Wakasugi, K.Ishimori, and I.Morishima (1997).
'Module'-substituted globins: artificial exon shuffling among myoglobin, hemoglobin alpha- and beta-subunits.
  Biophys Chem, 68, 265-273.  
8900144 T.Yamaguchi, J.Pang, K.S.Reddy, H.E.Witkowska, S.Surrey, and K.Adachi (1996).
Expression of soluble human beta-globin chains in bacteria and assembly in vitro with alpha-globin chains.
  J Biol Chem, 271, 26677-26683.  
7697717 C.D.Mol, A.S.Arvai, G.Slupphaug, B.Kavli, I.Alseth, H.E.Krokan, and J.A.Tainer (1995).
Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
  Cell, 80, 869-878.  
  7664751 M.M.Thayer, H.Ahern, D.Xing, R.P.Cunningham, and J.A.Tainer (1995).
Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
  EMBO J, 14, 4108-4120.
PDB code: 2abk
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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