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- PDB-2vrd: THE STRUCTURE OF THE ZINC FINGER FROM THE HUMAN SPLICEOSOMAL PROT... -

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Basic information

Entry
Database: PDB / ID: 2vrd
TitleTHE STRUCTURE OF THE ZINC FINGER FROM THE HUMAN SPLICEOSOMAL PROTEIN U1C
ComponentsU1 SMALL NUCLEAR RIBONUCLEOPROTEIN C
KeywordsNUCLEAR PROTEIN / RNA-BINDING PROTEIN / STRUCTURAL GENOMICS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / SPLICEOSOMAL PROTEIN / PHOSPHOPROTEIN / RIBONUCLEOPROTEIN / ZINC-FINGER / ZINC FINGER / METAL-BINDING / ZINC / RSGI / NUCLEUS / U1 SNRNP / RNA-BINDING
Function / homology
Function and homology information


commitment complex / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / mRNA 5'-splice site recognition / spliceosomal snRNP assembly / Cajal body / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome ...commitment complex / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / mRNA 5'-splice site recognition / spliceosomal snRNP assembly / Cajal body / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded RNA binding / mRNA binding / protein homodimerization activity / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein C / U1-C, C2H2-type zinc finger / U1 zinc finger / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Classic Zinc Finger / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Double Stranded RNA Binding Domain / Zinc finger C2H2 superfamily ...U1 small nuclear ribonucleoprotein C / U1-C, C2H2-type zinc finger / U1 zinc finger / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Classic Zinc Finger / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Double Stranded RNA Binding Domain / Zinc finger C2H2 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
U1 small nuclear ribonucleoprotein C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMuto, Y. / Pomeranz-Krummel, D. / Oubridge, C. / Hernandez, H. / Robinson, C. / Neuhaus, D. / Nagai, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Structure and Biochemical Properties of the Human Spliceosomal Protein U1C
Authors: Muto, Y. / Pomeranz-Krummel, D. / Oubridge, C. / Hernandez, H. / Robinson, C. / Neuhaus, D. / Nagai, K.
History
DepositionMar 31, 2008Deposition site: PDBE / Processing site: PDBE
SupersessionApr 8, 2008ID: 1UW2
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3452
Polymers7,2791
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)47 / 50LOW RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein U1 SMALL NUCLEAR RIBONUCLEOPROTEIN C / U1 SNRNP PROTEIN C / U1C PROTEIN / U1-C


Mass: 7279.186 Da / Num. of mol.: 1 / Fragment: ZINC FINGER DOMAIN, RESIDUES 1-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P09234
#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
111TOCSY
121NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY ON UNLABELLED U1C ZINC FINGER DOMAIN

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Sample preparation

DetailsContents: 90%WATER/10%D2O AND 100% D2O
Sample conditionspH: 6.5 / 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
X-PLORBRUNGERrefinement
XwinNMRstructure solution
Sparkystructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOW RESTRAINT VIOLATIONS / Conformers calculated total number: 50 / Conformers submitted total number: 47

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