[English] 日本語
Yorodumi
- PDB-1haj: A beta-Hairpin Structure in a 13-mer Peptide that Binds a-Bungaro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1haj
TitleA beta-Hairpin Structure in a 13-mer Peptide that Binds a-Bungarotoxin with High Affinity and Neutralizes its Toxicity
Components
  • ALPHA-BUNGAROTOXIN
  • PEPTIDE
KeywordsTOXIN/PEPTIDE / COMPLEX (TOXIN-PEPTIDE) / ACETYLCHOLINE RECEPTOR MIMITOPE / ALPHA-BUNGAROTOXIN / PROTEIN-PEPTIDE COMPLEX / TOXIN / BETA-HAIRPIN / TOXIN-PEPTIDE complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin/toxin-like / Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Alpha-bungarotoxin / Alpha-bungarotoxin
Similarity search - Component
Biological speciesBUNGARUS MULTICINCTUS (many-banded krait)
SYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING
AuthorsScherf, T. / Kasher, R. / Balass, M. / Fridkin, M. / Fuchs, S. / Katchalski-Katzir, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A Beta-Hairpin Structure in a 13-mer Peptide that Binds Alpha-Bungarotoxin with High Affinity and Neutralizes its Toxicity
Authors: Scherf, T. / Kasher, R. / Balass, M. / Fridkin, M. / Fuchs, S. / Katchalski-Katzir, E.
#1: Journal: Chem.Biol. / Year: 2001
Title: Design and Synthesis of Peptides that Bind A-Bungarotoxin with High Affinity
Authors: Kasher, R. / Balass, M. / Scherf, T. / Fridkin, M. / Fuchs, S. / Katchalski-Katzir, E.
History
DepositionApr 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Remark 700 SHEET DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM STRAND: S1A 1; STRANDS S2D & S2E FORM B- ... SHEET DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM STRAND: S1A 1; STRANDS S2D & S2E FORM B-HAIRPIN WITHIN THE BOUND PEPTIDE, THAT COMBINES TO S2A-S2C TO FORM 5-STRANDED INTERMOLECULAR BETA-SHEET.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA-BUNGAROTOXIN
B: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)9,7112
Polymers9,7112
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-8 kcal/mol
Surface area5530 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -NO RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein ALPHA-BUNGAROTOXIN / LONG NEUROTOXIN 1 / BGTX / ALPHA-BTX / A-BTX


Mass: 8005.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ALPHA-NEUROTOXIN / Source: (natural) BUNGARUS MULTICINCTUS (many-banded krait) / Secretion: VENOM / References: UniProt: P01378, UniProt: P60615*PLUS
#2: Protein/peptide PEPTIDE / / HIGH AFFINITY PEPTIDE


Mass: 1705.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MIMOTOPE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR / Source: (synth.) SYNTHETIC CONSTRUCT (others)
Compound detailsTHE PEPTIDE BINDS ALPHA-BUNGAROTOXIN AND THUS INHIBITS THE BINDING OF THE TOXIN TO THE NICOTINIC ...THE PEPTIDE BINDS ALPHA-BUNGAROTOXIN AND THUS INHIBITS THE BINDING OF THE TOXIN TO THE NICOTINIC RECEPTORS. THE OBSERVED QUATERNARY STATE IS MONOMERIC IN SOLUTION WHILE IN THE CRYSTAL STRUCTURES IT IS OBSERVED TO BE DIMERIC

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121HOHAHA
131DQF-COSY
NMR detailsText: THE STRUCTURES WERE DETERMINED USING STANDARD 2D 1H-NMR SPECTROSCOPY.

-
Sample preparation

DetailsContents: 1MM COMPLEX IN 90% WATER,10% D2O
Sample conditionspH: 6 / Pressure: AMBIENT / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS0.9BRUNGER, ADAMS, CLORE, DELANO, GROS ET ALrefinement
XWINNMRstructure solution
AURELIAstructure solution
CNSstructure solution
RefinementMethod: DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: RMS DEVIATIONS FROM IDEAL VALUES: BOND LENGTH (A) 0.0033,ANGLES (DEG) 0.52 IMPROPERS (DEG) 0.45
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATION / Conformers submitted total number: 10

+
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