[English] 日本語
Yorodumi
- PDB-2lwc: Met-enkephalin in DPMC SUV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lwc
TitleMet-enkephalin in DPMC SUV
ComponentsMet-enkephalin
KeywordsNEUROPEPTIDE / SUV DMPC
Function / homology
Function and homology information


synaptic vesicle lumen / chromaffin granule lumen / opioid peptide activity / neuronal dense core vesicle lumen / aggressive behavior / general adaptation syndrome, behavioral process / positive regulation of behavioral fear response / synaptic signaling via neuropeptide / symmetric synapse / G protein-coupled opioid receptor signaling pathway ...synaptic vesicle lumen / chromaffin granule lumen / opioid peptide activity / neuronal dense core vesicle lumen / aggressive behavior / general adaptation syndrome, behavioral process / positive regulation of behavioral fear response / synaptic signaling via neuropeptide / symmetric synapse / G protein-coupled opioid receptor signaling pathway / response to epinephrine / cell body fiber / cellular response to vitamin D / sensory perception / neuropeptide hormone activity / transmission of nerve impulse / startle response / locomotory exploration behavior / response to immobilization stress / behavioral fear response / neuropeptide signaling pathway / glial cell proliferation / cellular response to transforming growth factor beta stimulus / cellular response to cAMP / axon terminus / sensory perception of pain / Peptide ligand-binding receptors / Post-translational protein phosphorylation / response to nicotine / cellular response to virus / response to toxic substance / response to calcium ion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / osteoblast differentiation / response to estradiol / cellular response to oxidative stress / G alpha (i) signalling events / chemical synaptic transmission / perikaryon / response to lipopolysaccharide / response to ethanol / response to hypoxia / endoplasmic reticulum lumen / neuronal cell body / dendrite / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Proenkephalin A / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsMouret, L.
CitationJournal: To be Published
Title: Menk in DMPC SUV
Authors: Mouret, L.
History
DepositionJul 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 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
Revision 1.2May 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: Met-enkephalin


Theoretical massNumber of molelcules
Total (without water)5741
Polymers5741
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)20 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Met-enkephalin


Mass: 573.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01210

-
Experimental details

-
Experiment

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

-
Sample preparation

DetailsContents: 0.5 mM menk, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: menk-1
Sample conditionsIonic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

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

-
Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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