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- PDB-1ekz: NMR STRUCTURE OF THE COMPLEX BETWEEN THE THIRD DSRBD FROM DROSOPH... -

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Basic information

Entry
Database: PDB / ID: 1ekz
TitleNMR STRUCTURE OF THE COMPLEX BETWEEN THE THIRD DSRBD FROM DROSOPHILA STAUFEN AND A RNA HAIRPIN
Components
  • MATERNAL EFFECT PROTEIN (STAUFEN)
  • STAUFEN DOUBLE-STRANDED RNA BINDING DOMAIN
Keywordscell cycle/RNA / protein/RNA / protein dsRBD / Drosophila / RNA hairpin / cell cycle-RNA COMPLEX
Function / homology
Function and homology information


germ plasm / subsynaptic reticulum / pole plasm RNA localization / bicoid mRNA localization / regulation of oskar mRNA translation / pole plasm protein localization / posterior cell cortex / regulation of pole plasm oskar mRNA localization / asymmetric protein localization involved in cell fate determination / anterograde dendritic transport of messenger ribonucleoprotein complex ...germ plasm / subsynaptic reticulum / pole plasm RNA localization / bicoid mRNA localization / regulation of oskar mRNA translation / pole plasm protein localization / posterior cell cortex / regulation of pole plasm oskar mRNA localization / asymmetric protein localization involved in cell fate determination / anterograde dendritic transport of messenger ribonucleoprotein complex / neuroblast fate determination / positive regulation of cytoplasmic mRNA processing body assembly / pole plasm assembly / positive regulation of synaptic assembly at neuromuscular junction / neuronal ribonucleoprotein granule / RNA localization / basal cortex / anterior/posterior axis specification, embryo / apical cortex / intracellular mRNA localization / protein localization to synapse / oogenesis / lncRNA binding / germ cell development / long-term memory / dendrite cytoplasm / basal plasma membrane / mRNA 3'-UTR binding / P-body / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / apical part of cell / double-stranded RNA binding / cell cortex / neuron projection / apical plasma membrane / neuronal cell body / mRNA binding / plasma membrane / cytoplasm
Similarity search - Function
Staufen, C-terminal / : / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Maternal effect protein staufen
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR
AuthorsRamos, A. / Grunert, S. / Bycroft, M. / St Johnston, D. / Varani, G.
CitationJournal: EMBO J. / Year: 2000
Title: RNA recognition by a Staufen double-stranded RNA-binding domain.
Authors: Ramos, A. / Grunert, S. / Adams, J. / Micklem, D.R. / Proctor, M.R. / Freund, S. / Bycroft, M. / St Johnston, D. / Varani, G.
History
DepositionMar 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
B: STAUFEN DOUBLE-STRANDED RNA BINDING DOMAIN
A: MATERNAL EFFECT PROTEIN (STAUFEN)


Theoretical massNumber of molelcules
Total (without water)18,0772
Polymers18,0772
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)36 / 50structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: RNA chain STAUFEN DOUBLE-STRANDED RNA BINDING DOMAIN


Mass: 9612.737 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein MATERNAL EFFECT PROTEIN (STAUFEN) / DSRBDIII


Mass: 8463.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P25159

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 36

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