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- PDB-2ly2: NMR structure of the second and third lotus domains of tudor doma... -

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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 / Tudor domain profile. ...: / : / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tudor domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)20,3221
Polymers20,3221
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

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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

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Experimental details

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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

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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: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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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

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