[English] 日本語
Yorodumi
- PDB-7s3q: NMR Solution Structure of hGal(1-12)KK, a solubility-tagged trunc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s3q
TitleNMR Solution Structure of hGal(1-12)KK, a solubility-tagged truncation of the human neuropeptide galanin
ComponentsGalanin
KeywordsNEUROPEPTIDE / binding epitope / synthetic peptide
Function / homology
Function and homology information


galanin receptor binding / type 1 galanin receptor binding / type 2 galanin receptor binding / type 3 galanin receptor binding / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / positive regulation of timing of catagen / positive regulation of cortisol secretion / regulation of glucocorticoid metabolic process / negative regulation of lymphocyte proliferation ...galanin receptor binding / type 1 galanin receptor binding / type 2 galanin receptor binding / type 3 galanin receptor binding / galanin receptor activity / positive regulation of large conductance calcium-activated potassium channel activity / positive regulation of timing of catagen / positive regulation of cortisol secretion / regulation of glucocorticoid metabolic process / negative regulation of lymphocyte proliferation / neuropeptide hormone activity / feeding behavior / insulin secretion / response to immobilization stress / neuropeptide signaling pathway / cAMP-mediated signaling / protein kinase A signaling / Peptide ligand-binding receptors / secretory granule / response to insulin / response to estrogen / G alpha (i) signalling events / positive regulation of apoptotic process / response to xenobiotic stimulus / neuronal cell body / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Galanin / Galanin precursor / Galanin message associated peptide (GMAP) / Galanin / Galanin message associated peptide (GMAP) / Galanin signature. / Galanin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKraichely, K.N. / Hendy, C.M. / Parnham, S. / Giuliano, M.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103499-20 United States
CitationJournal: Biochemistry / Year: 2022
Title: Minimal Increments of Hydrophobic Collapse within the N-Terminus of the Neuropeptide Galanin.
Authors: Kraichely, K.N. / Clinkscales, S.E. / Hendy, C.M. / Mendoza, E.A. / Parnham, S. / Giuliano, M.W.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galanin


Theoretical massNumber of molelcules
Total (without water)1,5081
Polymers1,5081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Peptide state was determined to be monomeric after observation of no dispersion, broadening, or loss of resolution in peaks in its 1D 1H NMR spectrum over a 50- ...Evidence: assay for oligomerization, Peptide state was determined to be monomeric after observation of no dispersion, broadening, or loss of resolution in peaks in its 1D 1H NMR spectrum over a 50-fold range of concentration from 0.1 mM up to 5 mM.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Galanin


Mass: 1507.757 Da / Num. of mol.: 1 / Mutation: P45K, H46K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P22466
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H ROESY
141isotropic11D 1H acquisition

-
Sample preparation

DetailsType: solution
Contents: 5 mM hGal(2-12)KK, 4.14 mM D3 sodium acetate, 5.86 mM D4 acetic acid, 95% H2O/5% D2O
Details: 5 mM hGal(1-12)KK peptide 10 mM deuterated (d3/d4) sodium acetate/acetic acid buffer pH 4.6
Label: CMH-I-104A / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMhGal(2-12)KKnatural abundance1
4.14 mMsodium acetateD31
5.86 mMacetic acidD41
Sample conditionsDetails: 5 mM hGal(1-12)KK peptide 10 mM deuterated (d3/d4) sodium acetate/acetic acid buffer pH 4.6
Ionic strength: 4.14 mM sodium acetate-d3 mM / Label: 1 / pH: 4.6 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
MestreLab (Mnova / MestReNova / MestReC)MestreLab (Mnova / MestReNova / MestReC)chemical shift assignment
MestreLab (Mnova / MestReNova / MestReC)MestreLab (Mnova / MestReNova / MestReC)peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 25

+
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