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- PDB-1nxb: STRUCTURE AND FUNCTION OF SNAKE VENOM CURARIMIMETIC NEUROTOXINS -

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Basic information

Entry
Database: PDB / ID: 1nxb
TitleSTRUCTURE AND FUNCTION OF SNAKE VENOM CURARIMIMETIC NEUROTOXINS
ComponentsNEUROTOXIN B
KeywordsNEUROTOXIN (POST-SYNAPTIC)
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / 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: 1.38 Å
AuthorsTsernoglou, D. / Petsko, G.A.
Citation
Journal: Mol.Pharmacol. / Year: 1978
Title: Structure and function of snake venom curarimimetic neurotoxins.
Authors: Tsernoglou, D. / Petsko, G.A. / Hudson, R.A.
#1: Journal: Science / Year: 1977
Title: Molecular Graphics. Application to the Structure Determination of a Snake Venom Neurotoxin
Authors: Tsernoglou, D. / Petsko, G.A. / Mcqueenjunior, J.E. / Hermans, J.
#2: Journal: Biochim.Biophys.Acta / Year: 1977
Title: Protein Sequencing by Computer Graphics
Authors: Tsernoglou, D. / Petsko, G.A. / TU, A.T.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Three-Dimensional Structure of Neurotoxin a from Venom of the Philippines Sea Snake
Authors: Tsernoglou, D. / Petsko, G.A.
#4: Journal: FEBS Lett. / Year: 1976
Title: The Crystal Structure of a Post-Synaptic Neurotoxin from Sea Snake at 2.2 Angstroms Resolution
Authors: Tsernoglou, D. / Petsko, G.A.
History
DepositionAug 8, 1980Processing site: BNL
Revision 1.0Jan 27, 1981Provider: 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 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: NEUROTOXIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0703
Polymers6,8781
Non-polymers1922
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.900, 46.600, 21.300
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 NEUROTOXIN B


Mass: 6877.759 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: Q90VW1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN IS PROBABLY IDENTICAL TO ERABUTOXIN FROM JAPANESE SEA SNAKES. THIS POINT IS DISCUSSED ...THE PROTEIN IS PROBABLY IDENTICAL TO ERABUTOXIN FROM JAPANESE SEA SNAKES. THIS POINT IS DISCUSSED IN REFERENCES 3 AND 4 ABOVE.
Has protein modificationY
Nonpolymer detailsCOORDINATES FOR TWO SULFATE IONS ARE INCLUDED BELOW. THERE IS PROBABLY AT LEAST ONE OTHER BOUND ...COORDINATES FOR TWO SULFATE IONS ARE INCLUDED BELOW. THERE IS PROBABLY AT LEAST ONE OTHER BOUND SULFATE WHICH IS INCLUDED BELOW AS A WATER MOLECULE.
Sequence detailsRESIDUE NUMBERING IS SEQUENTIAL. IN PUBLISHED PAPERS A GENERAL HOMOLOGY SEQUENCE NUMBERING IS USED ...RESIDUE NUMBERING IS SEQUENTIAL. IN PUBLISHED PAPERS A GENERAL HOMOLOGY SEQUENCE NUMBERING IS USED OFTEN INSTEAD OF SEQUENTIAL NUMBERING OF RESIDUES. SEE REFERENCE 1 FOR DETAILS. RESIDUE 59 IS PROBABLY VALINE BUT THIS IS STILL UNDER INVESTIGATION. RESIDUES 18 AND 19 WERE ORDERED FROM THE 2.2 AND 1.38 ANGSTROM MAPS AFTER REFINEMENT. THE CHEMICAL SEQUENCE HAS THEM REVERSED. THE SAME IS TRUE OF RESIDUES 21 AND 22. SEE REFERENCE 3 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.64 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.38 Å
Refinement stepCycle: LAST / Highest resolution: 1.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms472 0 4 67 543

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