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- PDB-2mz1: Solution structure of hnRNP C RRM in complex with 5'-UUUUC-3' RNA -

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Basic information

Entry
Database: PDB / ID: 2mz1
TitleSolution structure of hnRNP C RRM in complex with 5'-UUUUC-3' RNA
Components
  • 5'-R(*UP*UP*UP*UP*C)-3'
  • Heterogeneous nuclear ribonucleoproteins C1/C2
KeywordsRNA BINDING PROTEIN/RNA / hnRNP C / RRM / complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


N6-methyladenosine-containing RNA reader activity / poly(U) RNA binding / telomerase holoenzyme complex / SUMOylation of RNA binding proteins / telomerase RNA binding / RHOBTB1 GTPase cycle / 3'-UTR-mediated mRNA stabilization / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of telomere maintenance via telomerase / RHOBTB2 GTPase cycle ...N6-methyladenosine-containing RNA reader activity / poly(U) RNA binding / telomerase holoenzyme complex / SUMOylation of RNA binding proteins / telomerase RNA binding / RHOBTB1 GTPase cycle / 3'-UTR-mediated mRNA stabilization / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of telomere maintenance via telomerase / 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 / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Heterogeneous nuclear ribonucleoproteins C1/C2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsCienikova, Z. / Damberger, F.F. / Hall, J. / Allain, F.H.-T. / Maris, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif.
Authors: Cienikova, Z. / Damberger, F.F. / Hall, J. / Allain, F.H. / Maris, C.
History
DepositionFeb 5, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoproteins C1/C2
B: 5'-R(*UP*UP*UP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)12,7772
Polymers12,7772
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Heterogeneous nuclear ribonucleoproteins C1/C2 / hnRNP C1/C2 / hnRNP C


Mass: 11291.922 Da / Num. of mol.: 1 / Fragment: RRM (UNP residues 2-106)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPC, HNRPC / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): codon+ / References: UniProt: P07910
#2: RNA chain 5'-R(*UP*UP*UP*UP*C)-3'


Mass: 1484.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D HN(CA)CO
1413D 1H-15N NOESY
1533D 1H-13C NOESY aliphatic
1633D 1H-13C edited-filtered NOESY
1732D 1H-1H TOCSY
1832D 1H-1H NOESY filtered-edited
1932D 1H-1H NOESY filtered-filtered

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 15N] hnRNP C, 1.0 mM 5'-R(*UP*UP*UP*UP*C)-3', 20 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] hnRNP C, 1.0 mM 5'-R(*UP*UP*UP*UP*C)-3', 20 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] hnRNP C, 1.0 mM 5'-R(*UP*UP*UP*UP*C)-3', 20 mM sodium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMhnRNP C-1[U-100% 15N]1
1.0 mM5'-R(*UP*UP*UP*UP*C)-3'-21
20 mMsodium phosphate-31
10 mMsodium chloride-41
1.0 mMhnRNP C-5[U-100% 13C; U-100% 15N]2
1.0 mM5'-R(*UP*UP*UP*UP*C)-3'-62
20 mMsodium phosphate-72
10 mMsodium chloride-82
1.0 mMhnRNP C-9[U-100% 13C; U-100% 15N]3
1.0 mM5'-R(*UP*UP*UP*UP*C)-3'-103
20 mMsodium phosphate-113
10 mMsodium chloride-123
Sample conditionsIonic strength: 0.040 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AVIIIBrukerAVIII6002
Bruker AVIIIBrukerAVIII7003
Bruker AVIIIBrukerAVIII5004

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1 / Details: ff99SB force-field
NMR constraintsNA alpha-angle constraints total count: 0 / NA beta-angle constraints total count: 0 / NA chi-angle constraints total count: 0 / NA delta-angle constraints total count: 4 / NA epsilon-angle constraints total count: 0 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 0 / NA sugar pucker constraints total count: 0 / NOE constraints total: 2775 / NOE intraresidue total count: 467 / NOE long range total count: 813 / NOE medium range total count: 659 / NOE sequential total count: 699 / Hydrogen bond constraints total count: 44
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.49 Å

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