[English] 日本語
Yorodumi
- PDB-8t01: Solution NMR structure of a multifunctional synthetic peptide Hp-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t01
TitleSolution NMR structure of a multifunctional synthetic peptide Hp-MAP3 derived from Temporin-PTa
ComponentsHp-MAP3 peptide
KeywordsANTIMICROBIAL PROTEIN
Function / homologydefense response to bacterium / extracellular region / Temporin-PTa
Function and homology information
Biological speciesPulchrana picturata (frog)
MethodSOLUTION NMR / simulated annealing
AuthorsFreitas, C.D.P. / Migliolo, L. / Silva, P.S. / Liao, L.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: To Be Published
Title: Solution NMR structure of a multifunctional synthetic peptide Hp-MAP3 derived from Temporin-PTa.
Authors: Freitas, C.D.P. / Migliolo, L. / Silva, P.S. / Liao, L.M.
History
DepositionMay 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hp-MAP3 peptide


Theoretical massNumber of molelcules
Total (without water)1,4831
Polymers1,4831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Hp-MAP3 peptide


Mass: 1483.021 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The Hp-MAP3 peptide is an analog derived from Temporin-PTa. The primary sequence of the parent peptide was used as a template for rational design, using amino acid residues for charge ...Details: The Hp-MAP3 peptide is an analog derived from Temporin-PTa. The primary sequence of the parent peptide was used as a template for rational design, using amino acid residues for charge modification and hydrophobicity. Thus obtaining an amphipathic peptide.
Source: (synth.) Pulchrana picturata (frog) / References: UniProt: P0C8U2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC

-
Sample preparation

DetailsType: solution
Contents: 1.5 mM Hp-MAP3 (peptide), 75 mM [U-98% 2H] SDS-d25, 0.05 % [U-98% 2H] DSS-D6, 90% H2O/10% D2O
Label: Hp-MAP3 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMHp-MAP3 (peptide)natural abundance1
75 mMSDS-d25[U-98% 2H]1
0.05 %DSS-D6[U-98% 2H]1
Sample conditionsIonic strength: neutral Not defined / Label: 1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
CcpNmr Analysis AssignCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 9

+
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