[English] 日本語
Yorodumi
- PDB-7qcb: Williams-Beuren syndrome related methyltransferase WBSCR27 in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qcb
TitleWilliams-Beuren syndrome related methyltransferase WBSCR27 in complex with SAH
ComponentsMethyltransferase-like 27
KeywordsTRANSFERASE / Williams-Beuren syndrome / SAM-dependent methyltransferase / Rossman fold / Class I methyltransferases
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase like 27
Function and homology information
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Mariasina, S.S. / Chang, C.-F. / Efimov, S.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-04-00318 Russian Federation
CitationJournal: Front Mol Biosci / Year: 2022
Title: Williams-Beuren Syndrome Related Methyltransferase WBSCR27: From Structure to Possible Function.
Authors: Mariasina, S.S. / Chang, C.F. / Navalayeu, T.L. / Chugunova, A.A. / Efimov, S.V. / Zgoda, V.G. / Ivlev, V.A. / Dontsova, O.A. / Sergiev, P.V. / Polshakov, V.I.
History
DepositionNov 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 20, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 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: Methyltransferase-like 27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3732
Polymers25,9881
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, NOE from the sample containing {13C,15N}-labeled SAH and {15N}-labeles WBSCR27.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12640 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein Methyltransferase-like 27 / Williams-Beuren syndrome critical region protein 27 / Williams-Beuren syndrome critical region ...Williams-Beuren syndrome critical region protein 27 / Williams-Beuren syndrome critical region protein 27 isoform alpha / Williams-Beuren syndrome critical region protein 27 isoform beta


Mass: 25988.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mettl27, BC002286, Wbscr27 / Plasmid: pET30aTEV-WBSCR27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BGM4
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
125isotropic22D 1H-15N HSQC
134isotropic23D HNCO
144isotropic23D HN(CA)CO
154isotropic23D HN(CO)CA
164isotropic23D HNCA
174isotropic23D CBCA(CO)NH
184isotropic23D HN(CA)CB
194isotropic23D HBHA(CO)NH
1104isotropic23D HNHAHB
1114isotropic23D 1H-15N TOCSY
1125isotropic23D (H)CCH-TOCSY
1135isotropic23D 1H-13C NOESY
1144isotropic53D 1H-13C NOESY
1154isotropic23D 15N-1H NOESY
1163anisotropic3IPAP
1177isotropic33D 15N-1H NOESY
1186isotropic42D 1H-13C HSQC
1191isotropic12D DQF-COSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-15N] WBSCR27, 10 mM SAH, 5 mM DTT, 0.2 % w/v sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N-wb27_sah_195% H2O/5% D2O
solution30.2 mM [U-15N] WBSCR27, 10 mM SAH, 5 mM DTT, 0.2 % w/v sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 0.225 % v/v phage Pf1 stock solution, 95% H2O/5% D2O15N-wb27_sah_RDC_Pf195% H2O/5% D2O
solution40.6 mM [U-95% 13C; U-99% 15N] WBSCR27, 0.6 mM SAH, 5 mM DTT, 0.2 % w/v sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N_13C_wb27_sah_h2o95% H2O/5% D2O
solution50.6 mM [U-95% 13C; U-99% 15N] WBSCR27, 0.6 mM SAH, 5 mM DTT, 0.2 % w/v sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 100% D2O15N_13C_wb27_sah_d2o100% D2O
solution60.3 mM [U-95% 15N] WBSCR27, 0.3 mM [U-95% 13C; U-99% 15N] SAH, 5 mM DTT, 0.2 % w/v sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 100% D2O15N-wb27_13C-SAH100% D2O
solution70.3 mM [U-95% 15N] WBSCR27, 0.3 mM [U-95% 13C; U-99% 15N] SAH, 5 mM DTT, 0.2 % w/v sodium azide, 50 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O15N-wb27_13CH3-Met-Thr95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMWBSCR27[U-15N]1
10 mMSAHnatural abundance1
5 mMDTTnatural abundance1
0.2 % w/vsodium azidenatural abundance1
50 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.2 mMWBSCR27[U-15N]3
10 mMSAHnatural abundance3
5 mMDTTnatural abundance3
0.2 % w/vsodium azidenatural abundance3
50 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
0.225 % v/vphage Pf1 stock solutionnatural abundance3
0.6 mMWBSCR27[U-95% 13C; U-99% 15N]4
0.6 mMSAHnatural abundance4
5 mMDTTnatural abundance4
0.2 % w/vsodium azidenatural abundance4
50 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
0.6 mMWBSCR27[U-95% 13C; U-99% 15N]5
0.6 mMSAHnatural abundance5
5 mMDTTnatural abundance5
0.2 % w/vsodium azidenatural abundance5
50 mMsodium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
0.3 mMWBSCR27[U-95% 15N]6
0.3 mMSAH[U-95% 13C; U-99% 15N]6
5 mMDTTnatural abundance6
0.2 % w/vsodium azidenatural abundance6
50 mMsodium phosphatenatural abundance6
50 mMsodium chloridenatural abundance6
0.3 mMWBSCR27[U-95% 15N]7
0.3 mMSAH[U-95% 13C; U-99% 15N]7
5 mMDTTnatural abundance7
0.2 % w/vsodium azidenatural abundance7
50 mMsodium phosphatenatural abundance7
50 mMsodium chloridenatural abundance7
Sample conditionsIonic strength: 100 mM / Label: condition1 / pH: 7 / PH err: 0.05 / Pressure: 1 atm / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Lomonosov MSU
Bruker AVANCEBrukerAVANCE8502Academia Sinica
Bruker AVANCEBrukerAVANCE8003Academia Sinica
Bruker AVANCEBrukerAVANCE7005Kazan Federal University
Bruker AVANCEBrukerAVANCE7004RUDN

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBrunger A. T. et.al.collection
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
PINE-SPARKYLee Wchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNS2.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRestPolshakov V.data analysis
RefinementMethod: simulated annealing / Software ordinal: 9
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / 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