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- PDB-2vy4: U11-48K CHHC ZN-FINGER DOMAIN -

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Basic information

Entry
Database: PDB / ID: 2vy4
TitleU11-48K CHHC ZN-FINGER DOMAIN
ComponentsU11/U12 SMALL NUCLEAR RIBONUCLEOPROTEIN 48 KDA PROTEIN
KeywordsSPLICING / MRNA PROCESSING / ALTERNATIVE SPLICING / TRANSCRIPTION / NUCLEUS / SPLICEOSOME / POLYMORPHISM / MRNA SPLICING
Function / homology
Function and homology information


U12-type spliceosomal complex / mRNA Splicing - Minor Pathway / RNA splicing / mRNA processing / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / U11-48K-like CHHC zinc finger / Zinc finger CHHC U11-48K-type profile. / Zinc finger C2H2 superfamily
Similarity search - Domain/homology
U11/U12 small nuclear ribonucleoprotein 48 kDa protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTidow, H. / Andreeva, A. / Rutherford, T.J. / Fersht, A.R.
CitationJournal: Structure / Year: 2009
Title: Solution structure of the U11-48K CHHC zinc-finger domain that specifically binds the 5' splice site of U12-type introns.
Authors: Tidow, H. / Andreeva, A. / Rutherford, T.J. / Fersht, A.R.
History
DepositionJul 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nmr_spectrometer.model
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U11/U12 SMALL NUCLEAR RIBONUCLEOPROTEIN 48 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2532
Polymers4,1881
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25LOWEST ENERGY, NO VIOLATIONS
RepresentativeModel #2

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Components

#1: Protein/peptide U11/U12 SMALL NUCLEAR RIBONUCLEOPROTEIN 48 KDA PROTEIN / U11/U12 SNRNP 48 KDA PROTEIN / U11/U12-48K / U11-48K CHHC ZN-FINGER


Mass: 4187.892 Da / Num. of mol.: 1 / Fragment: RESIDUES 53-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q6IEG0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HN(CA)CB
151CBCA
NMR detailsText: ASSIGNMENT USING TRIPLE-RESONANCE NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 25MM PHOSPHATE, PH7.2, 150MM NACL, 5MM DTT, 5%D2O
Sample conditionsIonic strength: 213 mM / pH: 7.2 / Pressure: 1.0 atm / Temperature: 298.0 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
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: DETAILS CAN BE FOUND IN CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY, NO VIOLATIONS / Conformers calculated total number: 25 / Conformers submitted total number: 20

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