[English] 日本語
Yorodumi
- PDB-1qk6: Solution structure of huwentoxin-I by NMR -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1qk6
TitleSolution structure of huwentoxin-I by NMR
ComponentsHUWENTOXIN-I
KeywordsTOXIN / HUWENTOXIN-I / SPIDER / CYSTINE KNOT
Function / homologyHuwentoxin, conserved site-1 / Huwentoxin-1 family / Ion channel inhibitory toxin / Huwentoxin-1 family signature. / other organism presynaptic membrane / other organism postsynaptic membrane / ion channel inhibitor activity / toxin activity / extracellular region / Mu/omega-theraphotoxin-Hs1a
Function and homology information
Specimen sourceSELENOCOSMIA HUWENA (Chinese earth tiger)
MethodSOLUTION NMR / distance geometry
AuthorsQu, Y. / Liang, S. / Ding, J. / Liu, X. / Zhang, R. / Gu, X.
Citation
Journal: J.Protein Chem. / Year: 1997
Title: Proton Nuclear Magnetic Resonance Studies on Huwentoxin-I from the Venom of the Spider Selenocosmia Huwena:2.Three-Dimensional Structure in Solution
Authors: Qu, Y. / Liang, S. / Ding, J. / Liu, X. / Zhang, R. / Gu, X.
#1: Journal: J.Protein Chem. / Year: 1995
Title: Proton Nuclear Magnetic Resonance Studies on Huwentoxin-I from the Venom of the Spider Selenocosmia Huwena:1.Sequence-Specific 1H-NMR Assignment
Authors: Qu, Y. / Liang, S. / Ding, J. / Ma, L. / Zhang, R. / Gu, X.
#2: Journal: Toxicon / Year: 1993
Title: Properties and Amino Acid Sequence of Huwentoxin-I, a Neurotoxin Purified from the Venom of the Chinese Bird Spider Selenocosmia Huwena
Authors: Liang, S. / Zhang, D. / Pan, X. / Chen, Q. / Zhou, P.
#3: Journal: J.Protein Chem. / Year: 1993
Title: Assignment of the Three Disulfide Bridges of Huwentoxin-I,A Neurotoxin from the Spider Selenocosmia Huwena
Authors: Zhang, D. / Liang, S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 10, 1999 / Release: Aug 20, 1999
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 20, 1999Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 16, 2019Structure modelData collection / Database referencescitation_citation.page_last
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUWENTOXIN-I


Theoretical massNumber of molelcules
Total (without water)3,7641
Polyers3,7641
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
Datacriteria
Number of conformers (submitted / calculated)10 / 50STEREOCHEMICAL ENERGY AND RESULT OF PROCHECK
RepresentativeModel #1

-
Components

#1: Protein/peptide HUWENTOXIN-I /


Mass: 3764.470 Da / Num. of mol.: 1 / Source: (natural) SELENOCOSMIA HUWENA (Chinese earth tiger) / Organ: VENOM GLAND / Secretion: VENOM / References: UniProt: P56676

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions IDExperiment IDSolution IDType
111COSY
121TOCSY
131NOESY
NMR detailsText: BEST PROCHECK RESULT. NULL

-
Sample preparation

DetailsContents: 10% WATER/90% D2O
sample conditionsIonic strength: 20 mM / pH: 5.0 / Pressure: 1 atm / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: STEREOCHEMICAL ENERGY AND RESULT OF PROCHECK
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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