[English] 日本語
Yorodumi
- PDB-1b1v: NMR STRUCTURE OF PSP1, PLASMATOCYTE-SPREADING PEPTIDE FROM PSEUDO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b1v
TitleNMR STRUCTURE OF PSP1, PLASMATOCYTE-SPREADING PEPTIDE FROM PSEUDOPLUSIA INCLUDENS
ComponentsPROTEIN (PLASMATOCYTE-SPREADING PEPTIDE)
KeywordsCYTOKINE / INSECT CYTOKINE / PLASMATOCYTE-SPREADING / EGF-LIKE
Function / homologyParalytic/GBP/PSP peptide / Paralytic/GBP/PSP peptide / cytokine activity / extracellular space / Plasmatocyte-spreading peptide
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVolkman, B.F. / Clark, K.D. / Anderson, M.E. / Pech, L.L. / Markley, J.L. / Strand, M.R.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Structure of the insect cytokine peptide plasmatocyte-spreading peptide 1 from Pseudoplusia includens.
Authors: Volkman, B.F. / Anderson, M.E. / Clark, K.D. / Hayakawa, Y. / Strand, M.R. / Markley, J.L.
History
DepositionNov 23, 1998Processing site: RCSB
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (PLASMATOCYTE-SPREADING PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)2,5121
Polymers2,5121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 60LOWEST TARGET FUNCTION
Representative

-
Components

#1: Protein/peptide PROTEIN (PLASMATOCYTE-SPREADING PEPTIDE) / PSP1


Mass: 2511.835 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN THE HEMOLYMPH TISSUE OF PSEUDOPLUSIA INCLUDENS (SOYBEAN LOOPER (MOTH)).
References: UniProt: O61704
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
NMR detailsText: BOTH: QUADRATURE IN INDIRECT DIM. WAS OBTAINED WITH STATES-TPPI. WATER SUPPRESION WAS ACHIEVED WITH A WATERGATE SEQ. WITH A 3-9-19 SELECTIVE INVERSION

-
Sample preparation

Sample conditionsIonic strength: 20 mM SODIUM PHOSPHATE / pH: 6 / Pressure: 1 atm / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX750BrukerDMX7507502

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5GUNTERT, MUMENTHALER, WUTHRICHrefinement
DYANAstructure solution
GARANTstructure solution
XEASYstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS ARE IN THE SUBMITTED FILES AND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 60 / Conformers submitted total number: 30

+
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