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- PDB-2vxf: Solution structure of the LSm-domain of zebrafish RAP55 -

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Basic information

Entry
Database: PDB / ID: 2vxf
TitleSolution structure of the LSm-domain of zebrafish RAP55
ComponentsLSM14A PROTEIN
KeywordsTRANSCRIPTION / LSM PROTEINS / TRANSLATIONAL REPRESSION / EDC3 / RAP55 / CAR-1 / P-BODIES / DECAPPING / MRNA DECAY
Function / homology
Function and homology information


P-body assembly / stress granule assembly / P-body / mRNA binding
Similarity search - Function
Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesDANIO RERIO (zebrafish)
MethodSOLUTION NMR / XPLOR
AuthorsTritschler, F. / Coles, M. / Truffault, V.
CitationJournal: Mol. Cell. Biol. / Year: 2008
Title: Similar modes of interaction enable Trailer Hitch and EDC3 to associate with DCP1 and Me31B in distinct protein complexes.
Authors: Tritschler, F. / Eulalio, A. / Helms, S. / Schmidt, S. / Coles, M. / Weichenrieder, O. / Izaurralde, E. / Truffault, V.
History
DepositionJul 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LSM14A PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,7041
Polymers10,7041
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 / 50MINIMUM ENERGY
RepresentativeModel #1

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Components

#1: Protein LSM14A PROTEIN / DANIO RERIO RAP55


Mass: 10704.024 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PEU-HIS / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q7SXR4
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO PRO
Sequence detailsMETHIONINE 1 IS REPLACED BY A PROLINE

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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
131HNCO
141HN(CA)CB
151CC(CO)NH
161(H)CC(CO)NH
171CBCA(CO)NH
181HBHA(CO)NH
191HCH-TOCSY
1101CCH- TOCSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 100 MM NACL, 10 MM BIS- TRIS, PH 7.0, 5 MM DTT, 90% H2O, 10% D2O
Sample conditionsIonic strength: 100 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 289.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.9.4BRUNGERrefinement
SPARKYstructure solution
RefinementMethod: XPLOR / Software ordinal: 1
Details: REFINEMENT AS BEEN DONE SIMILARLY TO THE N-TERMINAL LSM DOMAIN OF TRAL
NMR ensembleConformer selection criteria: MINIMUM ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 20

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