[English] 日本語
Yorodumi
- PDB-2ly2: NMR structure of the second and third lotus domains of tudor doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ly2
TitleNMR structure of the second and third lotus domains of tudor domain-containing protein 7 (NMR ensemble overlay for Lotus #3)
ComponentsTudor domain-containing protein 7
KeywordsRNA BINDING PROTEIN / TDRD7 / LOTUS DOMAIN / OST-HTH DOMAIN / RNA BINDING DOMAIN / GERMINAL GRANULES
Function / homology
Function and homology information


P granule organization / ribonucleoprotein granule / piRNA processing / lens morphogenesis in camera-type eye / chromatoid body / lens fiber cell differentiation / P granule / post-transcriptional regulation of gene expression / germ cell development / spermatogenesis ...P granule organization / ribonucleoprotein granule / piRNA processing / lens morphogenesis in camera-type eye / chromatoid body / lens fiber cell differentiation / P granule / post-transcriptional regulation of gene expression / germ cell development / spermatogenesis / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
TDRD7, third LOTUS domain / : / : / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / : / Tudor domain ...TDRD7, third LOTUS domain / : / : / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / : / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SNase-like, OB-fold superfamily / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tudor domain-containing protein 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsCui, G. / Botuyan, M. / Mer, G.
CitationJournal: To be Published
Title: NMR structure of the second and third lotus domains of tudor domain-containing protein 7
Authors: Cui, G. / Botuyan, M. / Mer, G.
History
DepositionSep 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tudor domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)20,3221
Polymers20,3221
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 Tudor domain-containing protein 7 / PCTAIRE2-binding protein / Tudor repeat associator with PCTAIRE 2 / Trap


Mass: 20322.172 Da / Num. of mol.: 1 / Fragment: LOTUS DOMAINS 2 and 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdrd7, Pctaire2bp / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K1H1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D CBCA(CO)NH
1613D HNCO
1713D HN(CA)CO
1813D H(CCO)NH
1913D C(CO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] TDRD7 (LOTUS1-LOTUS2), 90 % H2O, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTDRD7 (LOTUS1-LOTUS2)-1[U-100% 13C; U-100% 15N]1
90 %H2O-21
10 %D2O-31
Sample conditionsIonic strength: 0.26 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
XwinNMRBruker Biospincollection
SANEDuggan, Legge, Dyson & Wrightdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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