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PDBsum entry 1cdt
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protein ligands Protein-protein interface(s) links
Cytotoxin PDB id
1cdt

 

 

 

 

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Contents
Protein chains
60 a.a. *
Ligands
PO4 ×2
Waters ×48
* Residue conservation analysis
PDB id:
1cdt
Name: Cytotoxin
Title: Cardiotoxin v4/ii from naja mossambica mossambica: the refined crystal structure
Structure: Cardiotoxin vii4. Chain: a, b. Engineered: yes
Source: Naja mossambica. Mozambique cobra. Organism_taxid: 8644
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.197    
Authors: B.Rees,A.Bilwes,J.P.Samama,D.Moras
Key ref: B.Rees et al. (1990). Cardiotoxin VII4 from Naja mossambica mossambica. The refined crystal structure. J Mol Biol, 214, 281-297. PubMed id: 2370666
Date:
17-May-90     Release date:   15-Jul-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P01452  (3SA4_NAJMO) -  Cytotoxin 4 from Naja mossambica
Seq:
Struc: 		60 a.a.
60 a.a.
Key:    Secondary structure  CATH domain

 

 
J Mol Biol 214:281-297 (1990)
PubMed id: 2370666  
 
 
Cardiotoxin VII4 from Naja mossambica mossambica. The refined crystal structure.
B.Rees, A.Bilwes, J.P.Samama, D.Moras.
 
  ABSTRACT  
 
The crystal structure of cardiotoxin VII4 from Naja mossambica mossambica was refined to 2.5 A resolution. Fifty ordered solvent sites were localized and included in the refinement. The final R factor is 0.197 (lambda/(2sin theta) less than 5 A; F greater than 3 sigma). The three-dimensional structure is characterized by two beta-sheets. Of particular interest is the two-stranded beta-sheet in the N-terminal region. This shows a large right-handed twist and, though strongly connected to the core of the molecule, and in particular to the C-terminal end, protrudes out of the bulk of the molecule. The segment of four amino acid residues connecting the two strands of this sheet is particularly exposed. It contains an invariant proline residue that has probably an important structural role, and is completely hydrophobic. Two other conserved hydrophobic zones were identified; the largest extends over the second and third loops, on one side only of the molecule. All side-chains of invariant hydrophobic character (except proline residues) belong to one of these three zones. Also discussed are the dimeric assembly and the rather loose packing in the crystal. The three-dimensional structure is compared with that of short and long alpha-neurotoxins. Comparison with two-dimensional nuclear magnetic resonance results on the 68% homologous cardiotoxin CT X IIb shows an excellent overall agreement. A few differences are probably genuine.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18485004 A.Galat, G.Gross, P.Drevet, A.Sato, and A.Ménez (2008).
Conserved structural determinants in three-fingered protein domains.
  FEBS J, 275, 3207-3225.  
  18540072 R.Mir, M.Sinha, S.Sharma, N.Singh, P.Kaur, A.Srinivasan, and T.P.Singh (2008).
Isolation, purification, crystallization and preliminary crystallographic studies of sagitoxin, an oligomeric cardiotoxin from the venom of Naja naja saggitifera.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 545-547.  
15305029 H.Zhou, Q.Meng, L.Xie, and R.Zhang (2004).
A weak neurotoxin exhibits synergic effect with cardiotoxins when co-applied to two non-neural cell lines.
  Biol Pharm Bull, 27, 1241-1244.  
12019263 Y.Kamikubo, Y.Okumura, and D.J.Loskutoff (2002).
Identification of the disulfide bonds in the recombinant somatomedin B domain of human vitronectin.
  J Biol Chem, 277, 27109-27119.  
11053837 P.Kuhn, A.M.Deacon, S.Comoso, G.Rajaseger, R.M.Kini, I.Usón, and P.R.Kolatkar (2000).
The atomic resolution structure of bucandin, a novel toxin isolated from the Malayan krait, determined by direct methods.
  Acta Crystallogr D Biol Crystallogr, 56, 1401-1407.
PDB code: 1f94
10429199 D.V.Dementieva, E.V.Bocharov, and A.S.Arseniev (1999).
Two forms of cytotoxin II (cardiotoxin) from Naja naja oxiana in aqueous solution: spatial structures with tightly bound water molecules.
  Eur J Biochem, 263, 152-162.
PDB codes: 1cb9 1ccq
10089355 G.Spraggon (1999).
Envelope skeletonization as a means to determine monomer masks and non-crystallographic symmetry relationships: application in the solution of the structure of fibrinogen fragment D.
  Acta Crystallogr D Biol Crystallogr, 55, 458-463.  
10081963 J.A.Cuff, and G.J.Barton (1999).
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
  Proteins, 34, 508-519.  
9335337 T.M.Hall, J.A.Porter, K.E.Young, E.V.Koonin, P.A.Beachy, and D.J.Leahy (1997).
Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins.
  Cell, 91, 85-97.
PDB code: 1at0
  7613468 H.K.van den Born, Z.Radić, P.Marchot, P.Taylor, and I.Tsigelny (1995).
Theoretical analysis of the structure of the peptide fasciculin and its docking to acetylcholinesterase.
  Protein Sci, 4, 703-715.  
  7556055 J.G.Arnez, D.C.Harris, A.Mitschler, B.Rees, C.S.Francklyn, and D.Moras (1995).
Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate.
  EMBO J, 14, 4143-4155.
PDB code: 1htt
7601102 M.Dauplais, J.M.Neumann, S.Pinkasfeld, A.Ménez, and C.Roumestand (1995).
An NMR study of the interaction of cardiotoxin gamma from Naja nigricollis with perdeuterated dodecylphosphocholine micelles.
  Eur J Biochem, 230, 213-220.  
  8528070 M.Sukumar, J.Rizo, M.Wall, L.A.Dreyfus, Y.M.Kupersztoch, and L.M.Gierasch (1995).
The structure of Escherichia coli heat-stable enterotoxin b by nuclear magnetic resonance and circular dichroism.
  Protein Sci, 4, 1718-1729.
PDB code: 1ehs
7520819 C.M.Fletcher, R.A.Harrison, P.J.Lachmann, and D.Neuhaus (1994).
Structure of a soluble, glycosylated form of the human complement regulatory protein CD59.
  Structure, 2, 185-199.
PDB codes: 1cdq 1cdr 1cds
  8045252 M.Delarue, A.Poterszman, S.Nikonov, M.Garber, D.Moras, and J.C.Thierry (1994).
Crystal structure of a prokaryotic aspartyl tRNA-synthetase.
  EMBO J, 13, 3219-3229.  
8241426 B.Gilquin, C.Roumestand, S.Zinn-Justin, A.Ménez, and F.Toma (1993).
Refined three-dimensional solution structure of a snake cardiotoxin: analysis of the side-chain organization suggests the existence of a possible phospholipid binding site.
  Biopolymers, 33, 1659-1675.
PDB codes: 1cxn 1cxo
  7507750 C.M.Fletcher, R.A.Harrison, P.J.Lachmann, and D.Neuhaus (1993).
Sequence-specific 1H-NMR assignments and folding topology of human CD59.
  Protein Sci, 2, 2015-2027.  
8504828 J.F.O'Connell, P.E.Bougis, and K.Wüthrich (1993).
Determination of the nuclear-magnetic-resonance solution structure of cardiotoxin CTX IIb from Naja mossambica mossambica.
  Eur J Biochem, 213, 891-900.
PDB code: 2ccx
1544485 C.Jelsch, F.Lenfant, J.M.Masson, and J.P.Samama (1992).
Beta-lactamase TEM1 of E. coli. Crystal structure determination at 2.5 A resolution.
  FEBS Lett, 299, 135-142.  
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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