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- PDB-5ebx: THE CRYSTAL STRUCTURE OF ERABUTOXIN A AT 2.0 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 5ebx
TitleTHE CRYSTAL STRUCTURE OF ERABUTOXIN A AT 2.0 ANGSTROMS RESOLUTION
ComponentsERABUTOXIN A
KeywordsTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesLaticauda semifasciata (broad-banded blue sea krait)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsCorfield, P.W.R. / Lee, T.-J. / Low, B.W.
Citation
Journal: J.Biol.Chem. / Year: 1989
Title: The crystal structure of erabutoxin a at 2.0-A resolution.
Authors: Corfield, P.W. / Lee, T.J. / Low, B.W.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1988
Title: Refinement at 1.4 Angstroms Resolution of a Model of Erabutoxin B. Treatment of Ordered Solvent and Discrete Disorder
Authors: Smith, J.L. / Corfield, P.W.R. / Hendrickson, W.A. / Low, B.W.
#2: Journal: FEBS Lett. / Year: 1988
Title: Alpha-Toxin Binding to Acetylcholine Receptor Alpha 179-191 Peptides. Intrinsic Fluorescence Studies
Authors: Radding, W. / Corfield, P.W.R. / Levinson, L.S. / Hashim, G.A. / Low, B.W.
#3: Journal: Asia Pac.J.Pharmacol. / Year: 1987
Title: Acetylcholine Receptor. Alpha-Toxin Binding Site. Theoretical and Model Studies
Authors: Low, B.W. / Corfield, P.W.R.
#4: Journal: Eur.J.Biochem. / Year: 1985
Title: Erabutoxin B. Initial Protein Refinement and Sequence Analysis at 0.140 Nanometers Resolution
Authors: Bourne, P.E. / Sato, A. / Corfield, P.W.R. / Rosen, L.S. / Birken, S. / Low, B.W.
#5: Journal: Handb.Exp.Pharmacol. / Year: 1979
Title: The Three-Dimensional Structure of Postsynaptic Snake Neurotoxins. Consideration of Structure and Function
Authors: Low, B.W.
#6: Journal: J.Biol.Chem. / Year: 1971
Title: X-Ray Crystallographic Study of the Erabutoxins and of a Diiodo Derivative
Authors: Low, B.W. / Potter, R. / Jackson, R.B. / Tamiya, N. / Sato, S.
History
DepositionDec 20, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ERABUTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9502
Polymers6,8541
Non-polymers961
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.140, 46.970, 20.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ERABUTOXIN A


Mass: 6853.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Laticauda semifasciata (broad-banded blue sea krait)
References: UniProt: P60775
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsERABUTOXINS A AND B ARE SHORT-CHAIN POSTSYNAPTIC NEUROTOXINS ISOLATED FROM THE VENOM OF THE SEA- ...ERABUTOXINS A AND B ARE SHORT-CHAIN POSTSYNAPTIC NEUROTOXINS ISOLATED FROM THE VENOM OF THE SEA-SNAKE LATICAUDA SEMIFASCIA, FOUND OFF THE OKINAWAS. THE POSTSYNAPTIC NEUROTOXINS ARE ANTAGONISTS OF THE NICOTINIC ACETYLCHOLINE RECEPTOR. HOMOLOGY EXISTS BETWEEN ALL THESE VENOM NEUROTOXINS FOR BOTH SHORT AND LONG CHAIN SERIES. (SEE REFERENCE 6 ABOVE FOR DETAILS). THE CLOSE STRUCTURAL SIMILARITY BETWEEN EA AND EB, PARTICULARLY BETWEEN THE EA AND EB REACTIVE SITE DOMAINS, SUPPORTS THE HIGH RESOLUTION EB STRUCTURE AS A VALID PROTOTYPE FOR ALL OF THE POSTSYNAPTIC NEUROTOXINS OF THE SHORT SNAKE VENOM SERIES. IN ADDITION, THE SPECIFIC ROLE PROPOSED (REFERENCE 4) FOR THE HIGHLY MOBILE PERIPHERAL SEGMENT PRO 44 - GLY 49 IN NEUROTOXIN BINDING TO THE ACETYLCHOLINE RECEPTOR, IS SUPPORTED BY THE DISTRIBUTION OF THERMAL PARAMETERS IN THIS REGION OF EA.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.39 %
Crystal grow
*PLUS
Method: microdialysis
Details: referred to 'Tamiya.', (1966) Biochem.J., 99, 624-630
Components of the solutions
*PLUS
Conc.: 0.85 % / Common name: sodium chloride

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 2714 / % possible obs: 75 % / Observed criterion σ(I): 2 / Num. measured all: 3640

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→10 Å / σ(I): 2 /
RfactorNum. reflection
obs0.168 2680
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 0 5 62 543
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0260.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6611.5
X-RAY DIFFRACTIONp_mcangle_it1.12
X-RAY DIFFRACTIONp_scbond_it1.2762
X-RAY DIFFRACTIONp_scangle_it1.9863
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.130.2
X-RAY DIFFRACTIONp_multtor_nbd0.150.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1440.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor19.815
X-RAY DIFFRACTIONp_orthonormal_tor15.920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 2680 / σ(I): 2 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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