[English] 日本語
Yorodumi
- PDB-2mcr: Solution structure of ShK-like immunomodulatory peptide from Brug... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mcr
TitleSolution structure of ShK-like immunomodulatory peptide from Brugia malayi (filarial worm)
ComponentsProbable zinc metalloproteinase, putative
KeywordsIMMUNE SYSTEM / worms / BmK1 / ShK-like peptide / Kv1.3
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / zinc ion binding
Similarity search - Function
ShK toxin domain / ShK domain-like / Astacin-like metallopeptidase domain / ShKT domain / ShKT domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Metalloendopeptidase / :
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsChhabra, S. / Swarbrick, J.D. / Pennington, M.W. / Chang, S.C. / Norton, R.S.
CitationJournal: Faseb J. / Year: 2014
Title: Kv1.3 channel-blocking immunomodulatory peptides from parasitic worms: implications for autoimmune diseases.
Authors: Chhabra, S. / Chang, S.C. / Nguyen, H.M. / Huq, R. / Tanner, M.R. / Londono, L.M. / Estrada, R. / Dhawan, V. / Chauhan, S. / Upadhyay, S.K. / Gindin, M. / Hotez, P.J. / Valenzuela, J.G. / ...Authors: Chhabra, S. / Chang, S.C. / Nguyen, H.M. / Huq, R. / Tanner, M.R. / Londono, L.M. / Estrada, R. / Dhawan, V. / Chauhan, S. / Upadhyay, S.K. / Gindin, M. / Hotez, P.J. / Valenzuela, J.G. / Mohanty, B. / Swarbrick, J.D. / Wulff, H. / Iadonato, S.P. / Gutman, G.A. / Beeton, C. / Pennington, M.W. / Norton, R.S. / Chandy, K.G.
History
DepositionAug 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable zinc metalloproteinase, putative


Theoretical massNumber of molelcules
Total (without water)4,1831
Polymers4,1831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Probable zinc metalloproteinase, putative


Mass: 4182.894 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Brugia malayi (agent of lymphatic filariasis)
References: UniProt: A8PQK5, UniProt: A0A0J9XQE3*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-15N HSQC
2212D 1H-13C HSQC
2322D 1H-1H NOESY
1422D 1H-1H NOESY
2522D 1H-1H TOCSY
2612D DQF-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM entity, 10 mM sodium phosphate, 100 % D2O, 100% D2O100% D2O
20.8 mM entity, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.8 mMentity-11
10 mMsodium phosphate-21
100 %D2O-31
0.8 mMentity-42
10 mMsodium phosphate-52
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.8 ambient 293 K
24.8 ambient 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
CcpNmrCCPNchemical shift assignment
TopSpin3.2Bruker Biospincollection
XPLOR_NIHBRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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