[English] 日本語
Yorodumi
- PDB-2rqk: NMR Solution Structure of Mesoderm Development (MESD) - closed co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rqk
TitleNMR Solution Structure of Mesoderm Development (MESD) - closed conformation
ComponentsMesoderm development candidate 2
KeywordsCHAPERONE
Function / homology
Function and homology information


positive regulation of skeletal muscle acetylcholine-gated channel clustering / protein localization to cell surface / low-density lipoprotein particle receptor binding / mesoderm development / phagocytosis / ossification / Wnt signaling pathway / protein folding / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
LRP chaperone MESD / Chaperone for wingless signalling and trafficking of LDL receptor / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsNMR based model structure of the conserved core region of mesoderm development (D45-K184). Flexible ...NMR based model structure of the conserved core region of mesoderm development (D45-K184). Flexible loop region (D71-K103) is ommitted.
AuthorsKoehler, C. / Lighthouse, J.K. / Werther, T. / Andersen, O.M. / Diehl, A. / Schmieder, P. / Holdener, B.C. / Oschkinat, H.
CitationJournal: Structure / Year: 2011
Title: The Structure of MESD45-184 Brings Light into the Mechanism of LDLR Family Folding
Authors: Kohler, C. / Lighthouse, J.K. / Werther, T. / Andersen, O.M. / Diehl, A. / Schmieder, P. / Du, J. / Holdener, B.C. / Oschkinat, H.
History
DepositionAug 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mesoderm development candidate 2


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Mesoderm development candidate 2


Mass: 16148.112 Da / Num. of mol.: 1
Fragment: D45-K184 conserved core region, UNP residues 45-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mesdc2 / Plasmid: pET-30 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ERE7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR based model structure of the conserved core region of mesoderm development (D45-K184). Flexible loop region (D71-K103) is ommitted.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1242D 1H-15N HSQC
1312D 1H-13C HSQC
1423D CBCA(CO)NH
1523D CBCANNH
1623D HNCO
1723D HN(CA)CO
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11023D H(CCCO)NH-TOCSY
11123D (H)CC(CO)NH-TOCSY
11233D 1H-15N NOESY
11313D 1H-13C NOESY
11432D 1H-15N HSQC coupled
11532D 1H-15N HSQC 15N T1-edited
11632D 1H-15N HSQC 15N T2-edited

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-100% 13C; U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 100% D2O100% D2O
21mM [U-100% 13C; U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31mM [U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
41mM [U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMESD[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
0.02 %sodium azide1
0.1 mMEDTA1
1 mMMESD[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
0.02 %sodium azide2
0.1 mMEDTA2
1 mMMESD[U-100% 15N]3
20 mMsodium phosphate3
50 mMsodium chloride3
0.02 %sodium azide3
0.1 mMEDTA3
1 mMMESD[U-100% 15N]4
20 mMsodium phosphate4
50 mMsodium chloride4
0.02 %sodium azide4
0.1 mMEDTA4
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVBrukerAV9001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddardpeak picking
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
CYANA2Guntert, Mumenthaler, Wuthrichstructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra, Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 656 / NOE intraresidue total count: 0 / NOE long range total count: 252 / NOE medium range total count: 108 / NOE sequential total count: 296 / Hydrogen bond constraints total count: 106 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 113 / Protein psi angle constraints total count: 113
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

+
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