[English] 日本語
Yorodumi
- PDB-7voz: Solution structure of cecropin P1(1-29) in dodecylphosphocholine ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7voz
TitleSolution structure of cecropin P1(1-29) in dodecylphosphocholine micelles
ComponentsCecropin-P1
KeywordsANTIMICROBIAL PROTEIN / cecropin P1 / calmodulin-fusion / antimicrobial peptides
Function / homologyantimicrobial peptide secretion / Cecropin family signature. / Cecropin / Cecropin family / antibacterial humoral response / defense response to bacterium / extracellular region / Cecropin-P1
Function and homology information
Biological speciesAscaris suum (pig roundworm)
MethodSOLUTION NMR / simulated annealing
AuthorsGu, H. / Kumeta, H. / Aizawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Omega / Year: 2022
Title: Three-Dimensional Structure of the Antimicrobial Peptide Cecropin P1 in Dodecylphosphocholine Micelles and the Role of the C-Terminal Residues
Authors: Gu, H. / Kato, T. / Kumeta, H. / Kumaki, Y. / Tsukamoto, T. / Kikukawa, T. / Demura, M. / Ishida, H. / Vogel, H.J. / Aizawa, T.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cecropin-P1


Theoretical massNumber of molelcules
Total (without water)3,0921
Polymers3,0921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Cecropin-P1


Mass: 3091.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Gene: ASCEC-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14661

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
121anisotropic12D 1H-13C HSQC
131anisotropic12D 1H-1H NOESY
141anisotropic13D 1H-13C NOESY
151anisotropic13D CBCA(CO)NH
1121anisotropic13D C(CO)NH
1111anisotropic13D HNCA
1101anisotropic13D HN(CA)CB
191anisotropic13D HN(CO)CA
181anisotropic13D HNCO
171anisotropic13D HBHA(CO)NH
161anisotropic13D (H)CCH-TOCSY

-
Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] Cecropin P1 (1-29), 40 mM [U-2H] DPC, 90% H2O/10% D2O
Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCecropin P1 (1-29)[U-13C; U-15N]1
40 mMDPC[U-2H]1
Sample conditionsIonic strength: 42 mM / Label: conditions_1 / pH: 5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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