[English] 日本語
Yorodumi
- PDB-2mnw: Solution structure of the P22S mutant of N-terminal CS domain of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mnw
TitleSolution structure of the P22S mutant of N-terminal CS domain of human Shq1
ComponentsProtein SHQ1 homolog
KeywordsPROTEIN BINDING / Dyskerin / Cbf5 / H/ACA
Function / homology
Function and homology information


box H/ACA snoRNP assembly / telomerase RNA localization to Cajal body / regulation of androgen receptor signaling pathway / Telomere Extension By Telomerase / protein-RNA complex assembly / positive regulation of TORC1 signaling / unfolded protein binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like ...Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein SHQ1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSingh, M. / Wang, Z. / Cascio, D. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure and Interactions of the CS Domain of Human H/ACA RNP Assembly Protein Shq1.
Authors: Singh, M. / Wang, Z. / Cascio, D. / Feigon, J.
History
DepositionApr 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Jun 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
Revision 1.3May 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: Protein SHQ1 homolog


Theoretical massNumber of molelcules
Total (without water)14,6111
Polymers14,6111
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein SHQ1 homolog


Mass: 14611.280 Da / Num. of mol.: 1 / Fragment: CS domain (UNP residues 1-96) / Mutation: P22S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHQ1 / Plasmid: pET41 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PI26

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D C(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D HN(CO)CA
1933D (H)CCH-TOCSY
11023D (H)CCH-TOCSY
11123D HBHA(CO)NH
11233D 1H-13C NOESY aliphatic
11323D 1H-15N NOESY
11433D 1H-13C NOESY aromatic
11513D HNHA
11623D HCACO
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data.

-
Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.5-1 mM [U-15N] P22S mutant of human Shq1 CS domain, 95% H2O/5% D2O95% H2O/5% D2O
220 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.5-1 mM [U-99% 13C; U-99% 15N] P22S mutant of human Shq1 CS domain, 95% H2O/5% D2O95% H2O/5% D2O
320 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 0.5-1 mM [U-99% 13C; U-99% 15N] P22S mutant of human Shq1 CS domain, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMsodium phosphate-11
100 mMsodium chloride-21
1 mMDTT-31
mMP22S mutant of human Shq1 CS domain-4[U-15N]0.5-11
20 mMsodium phosphate-52
100 mMsodium chloride-62
1 mMDTT-72
mMP22S mutant of human Shq1 CS domain-8[U-99% 13C; U-99% 15N]0.5-12
20 mMsodium phosphate-93
100 mMsodium chloride-103
1 mMDTT-113
mMP22S mutant of human Shq1 CS domain-12[U-99% 13C; U-99% 15N]0.5-13
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
XwinNMRBruker Biospindata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2852 / NOE intraresidue total count: 674 / NOE long range total count: 1006 / NOE medium range total count: 329 / NOE sequential total count: 843
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
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