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- PDB-2diq: Solution structure of the TUDOR domain of Tudor and KH domain con... -

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Basic information

Entry
Database: PDB / ID: 2diq
TitleSolution structure of the TUDOR domain of Tudor and KH domain containing protein
ComponentsTudor and KH domain-containing protein
KeywordsRNA BINDING PROTEIN / TUDOR domain / Tudor and KH domain containing protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


piP-body / pi-body / P granule organization / piRNA processing / male meiotic nuclear division / fertilization / P granule / PIWI-interacting RNA (piRNA) biogenesis / spermatogenesis / mitochondrion / RNA binding
Similarity search - Function
: / : / : / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain ...: / : / : / : / Tudor domain / Tudor domain profile. / KH domain / K Homology domain, type 1 / Tudor domain / Tudor domain / Type-1 KH domain profile. / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / K Homology domain, type 1 superfamily / SH3 type barrels. / K Homology domain / K homology RNA-binding domain / Roll / Mainly Beta
Similarity search - Domain/homology
Tudor and KH domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the TUDOR domain of Tudor and KH domain containing protein
Authors: Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S.
History
DepositionMar 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tudor and KH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)11,8231
Polymers11,8231
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Tudor and KH domain-containing protein


Mass: 11823.083 Da / Num. of mol.: 1 / Fragment: TUDOR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell free protein synthesis / Gene: TDRKH, TDRD2 / Plasmid: P050905-13 / Production host: Cell free synthesis / References: UniProt: Q9Y2W6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.9321Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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