[English] 日本語
Yorodumi
- PDB-2h7z: Crystal structure of irditoxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h7z
TitleCrystal structure of irditoxin
Components
  • Irditoxin subunit A
  • Irditoxin subunit B
KeywordsTOXIN / three-finger toxin / neurotoxin / snake venom
Function / homology
Function and homology information


modulation of receptor activity in another organism / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Irditoxin subunit A / Irditoxin subunit B
Similarity search - Component
Biological speciesBoiga irregularis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsPawlak, J. / Kini, R.M. / Stura, E.A. / Le Du, M.H.
Citation
Journal: Faseb J. / Year: 2009
Title: Irditoxin, a novel covalently linked heterodimeric three-finger toxin with high taxon-specific neurotoxicity.
Authors: Pawlak, J. / Mackessy, S.P. / Sixberry, N.M. / Stura, E.A. / Le Du, M.H. / Menez, R. / Foo, C.S. / Menez, A. / Nirthanan, S. / Kini, R.M.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Denmotoxin, a three-finger toxin from the colubrid snake Boiga dendrophila (Mangrove Catsnake) with bird-specific activity.
Authors: Pawlak, J. / Mackessy, S.P. / Fry, B.G. / Bhatia, M. / Mourier, G. / Fruchart-Gaillard, C. / Servent, D. / Menez, R. / Stura, E. / Menez, A. / Kini, R.M.
History
DepositionJun 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Database references
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Irditoxin subunit A
B: Irditoxin subunit B


Theoretical massNumber of molelcules
Total (without water)17,1122
Polymers17,1122
Non-polymers00
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.679, 52.106, 45.031
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Irditoxin subunit A


Mass: 8406.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Boiga irregularis (snake) / References: UniProt: A0S864
#2: Protein Irditoxin subunit B


Mass: 8705.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Boiga irregularis (snake) / References: UniProt: A0S865
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 5000, 100mM NaBr, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.006768 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006768 Å / Relative weight: 1
ReflectionResolution: 1.1→52 Å / Num. obs: 53091 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.1→1.12 Å / % possible all: 44.4

-
Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
MLPHAREphasing
REFMAC5.1.24refinement
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→45 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.2399 2092 RANDOM
Rwork0.2142 --
obs0.216 41024 -
all-43116 -
Refinement stepCycle: LAST / Resolution: 1.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 442 1620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011004
X-RAY DIFFRACTIONr_angle_refined_deg1.77049

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more