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- PDB-1txp: Heterogeneous Nuclear Ribonucleoprotein (hnRNP) C Oligomerization... -

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Basic information

Entry
Database: PDB / ID: 1txp
TitleHeterogeneous Nuclear Ribonucleoprotein (hnRNP) C Oligomerization Domain Tetramer
ComponentsHeterogeneous Nuclear Ribonucleoprotein C protein
KeywordsSIGNALING PROTEIN / Antiparallel Four Helix Coiled Coil Tetramer hnRNPC
Function / homology
Function and homology information


N6-methyladenosine-containing RNA reader activity / telomerase RNA binding / telomerase holoenzyme complex / SUMOylation of RNA binding proteins / poly(U) RNA binding / RHOBTB1 GTPase cycle / 3'-UTR-mediated mRNA stabilization / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / RHOBTB2 GTPase cycle ...N6-methyladenosine-containing RNA reader activity / telomerase RNA binding / telomerase holoenzyme complex / SUMOylation of RNA binding proteins / poly(U) RNA binding / RHOBTB1 GTPase cycle / 3'-UTR-mediated mRNA stabilization / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / RHOBTB2 GTPase cycle / nucleosomal DNA binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / osteoblast differentiation / actin cytoskeleton / chromatin remodeling / chromatin / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
Heterogeneous nuclear ribonucleoprotein C / : / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoproteins C1/C2 / Heterogeneous nuclear ribonucleoproteins C1/C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWhitson, S.R. / Lestourgeon, W.M. / Krezel, A.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Solution Structure of the Symmetric Coiled Coil Tetramer Formed by the Oligomerization Domain of hnRNP C: Implications for Biological Function.
Authors: Whitson, S.R. / Lestourgeon, W.M. / Krezel, A.M.
History
DepositionJul 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous Nuclear Ribonucleoprotein C protein
B: Heterogeneous Nuclear Ribonucleoprotein C protein
C: Heterogeneous Nuclear Ribonucleoprotein C protein
D: Heterogeneous Nuclear Ribonucleoprotein C protein


Theoretical massNumber of molelcules
Total (without water)13,2644
Polymers13,2644
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide
Heterogeneous Nuclear Ribonucleoprotein C protein / hnRNP C


Mass: 3315.893 Da / Num. of mol.: 4 / Fragment: Oligomerization Domain / Mutation: L180I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HnRNP C1 / Plasmid: pET32(LIC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q86U45, UniProt: P07910*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM monomer; 90% H2O, 10% D2O90% H2O/10% D2O
22 mM 15N-monomer; 90% H2O, 10% D2O90% H2O/10% D2O
32 mM 15N/13C-monomer; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0 mM NaCl / pH: 6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Bruker softwarecollection
XwinNMR3Bruker softwareprocessing
XEASY1.3.13Bartels et al.data analysis
CYANA1.0.6Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures are based on 1628 total constraints, including 1308 NOE-derived distance constraints, 244 dihedral angle restraints and 76 hydrogen bond distance restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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