[English] 日本語
Yorodumi
- PDB-2naw: NMR solution structure of Exendin-4/conotoxin chimera (Ex-4[1-27]... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2naw
TitleNMR solution structure of Exendin-4/conotoxin chimera (Ex-4[1-27]/pl14a)
ComponentsExendin-4, Alpha/kappa-conotoxin pl14a chimera
KeywordsTOXIN / agonist
Function / homologyGlucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / hormone activity / regulation of blood pressure / toxin activity / extracellular region / Exendin-4
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSchroeder, C.I. / Swedberg, J.E. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Truncated Glucagon-like Peptide-1 and Exendin-4 alpha-Conotoxin pl14a Peptide Chimeras Maintain Potency and alpha-Helicity and Reveal Interactions Vital for cAMP Signaling in Vitro.
Authors: Swedberg, J.E. / Schroeder, C.I. / Mitchell, J.M. / Fairlie, D.P. / Edmonds, D.J. / Griffith, D.A. / Ruggeri, R.B. / Derksen, D.R. / Loria, P.M. / Price, D.A. / Liras, S. / Craik, D.J.
History
DepositionJan 12, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references / Structure summary
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Aug 17, 2016Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exendin-4, Alpha/kappa-conotoxin pl14a chimera


Theoretical massNumber of molelcules
Total (without water)4,4961
Polymers4,4961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Exendin-4, Alpha/kappa-conotoxin pl14a chimera


Mass: 4496.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P26349*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC

-
Sample preparation

DetailsContents: 0.2 mM H2O, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: H2O-1
Sample conditionspH: 3.6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
TopSpinBruker Biospincollection
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.chemical shift calculation
XEASYBartels et al.peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 506 / NOE intraresidue total count: 154 / NOE long range total count: 35 / NOE medium range total count: 122 / NOE sequential total count: 195 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 38 / Protein phi angle constraints total count: 19 / Protein psi angle constraints total count: 19
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

+
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