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- PDB-2km8: Interdomain RRM packing contributes to RNA recognition in the rna... -

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Basic information

Entry
Database: PDB / ID: 2km8
TitleInterdomain RRM packing contributes to RNA recognition in the rna15, hrp1, anchor RNA 3' processing ternary complex
Components
  • 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
  • Nuclear polyadenylated RNA-binding protein 4
  • mRNA 3'-end-processing protein RNA15
KeywordsRNA binding protein/RNA / 3' processing / RRM domain / rna15p / hrp1p / enhancer element / positioning element / RNA recognition / mRNA processing / Nucleus / RNA-binding / Nonsense-mediated mRNA decay / Phosphoprotein / RNA binding protein-RNA COMPLEX
Function / homology
Function and homology information


mRNA cleavage stimulating factor complex / response to DNA damage checkpoint signaling / mRNA cleavage factor complex / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mRNA processing / cytoplasmic stress granule / molecular adaptor activity / mRNA binding ...mRNA cleavage stimulating factor complex / response to DNA damage checkpoint signaling / mRNA cleavage factor complex / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mRNA processing / cytoplasmic stress granule / molecular adaptor activity / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
HRP1, RNA recognition motif 1 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / 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 ...HRP1, RNA recognition motif 1 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / 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 / RNA (> 10) / mRNA 3'-end-processing protein RNA15 / Nuclear polyadenylated RNA-binding protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLeeper, T.C. / Varani, G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Novel Protein-Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1.
Authors: Leeper, T.C. / Qu, X. / Lu, C. / Moore, C. / Varani, G.
History
DepositionJul 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
B: mRNA 3'-end-processing protein RNA15
C: Nuclear polyadenylated RNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)32,5133
Polymers32,5133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'


Mass: 4096.478 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein mRNA 3'-end-processing protein RNA15 / rna15p


Mass: 9350.483 Da / Num. of mol.: 1 / Fragment: UNP residues 14 to 97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: 2.1, RNA15, YGL044C / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys / References: UniProt: P25299
#3: Protein Nuclear polyadenylated RNA-binding protein 4 / Cleavage factor IB / CFIB / hrp1p


Mass: 19065.559 Da / Num. of mol.: 1 / Fragment: UNP residues 156 to 322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HRP1, NAB4, NAB5, YOL123W / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys / References: UniProt: Q99383

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of rna15p and hrp1p proteins bound to RNA refined with PREs and RDCs.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
1532D 1H-13C HSQC
1642D 1H-13C HSQC
1752D 1H-13C HSQC
1853D HNCO
1953D HNCA
11053D HN(CA)CB
11153D HN(CO)CA
11253D CBCA(CO)NH
11353D (H)CCH-TOCSY
11453D 1H-15N TOCSY
11553D 1H-15N NOESY
11653D 1H-13C NOESY
11763D 1H-15N NOESY
11863D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N] rna15p-1, 0.4 mM hrp1p-2, 0.4 mM anchor RNA-3, 93% H2O/7% D2O93% H2O/7% D2O
20.6 mM rna15p-4, 0.6 mM [U-100% 15N] hrp1p-5, 0.6 mM anchor RNA-6, 93% H2O/7% D2O93% H2O/7% D2O
30.35 mM [U-100% 13C] rna15p-7, 0.35 mM [U-100% 15N] hrp1p-8, 0.35 mM anchor RNA-9, 93% H2O/7% D2O93% H2O/7% D2O
40.5 mM [U-100% 15N] rna15p-10, 0.5 mM [U-100% 13C] hrp1p-11, 0.5 mM anchor RNA-12, 93% H2O/7% D2O93% H2O/7% D2O
50.5 mM [U-100% 13C; U-100% 15N] rna15p-13, 0.5 mM hrp1p-14, 0.5 mM anchor RNA-15, 93% H2O/7% D2O93% H2O/7% D2O
60.5 mM rna15p-16, 0.5 mM [U-100% 13C; U-100% 15N] hrp1p-17, 0.5 mM anchor RNA-18, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMrna15p-1[U-100% 15N]1
0.4 mMhrp1p-21
0.4 mManchor RNA-31
0.6 mMrna15p-42
0.6 mMhrp1p-5[U-100% 15N]2
0.6 mManchor RNA-62
0.35 mMrna15p-7[U-100% 13C]3
0.35 mMhrp1p-8[U-100% 15N]3
0.35 mManchor RNA-93
0.5 mMrna15p-10[U-100% 15N]4
0.5 mMhrp1p-11[U-100% 13C]4
0.5 mManchor RNA-124
0.5 mMrna15p-13[U-100% 13C; U-100% 15N]5
0.5 mMhrp1p-145
0.5 mManchor RNA-155
0.5 mMrna15p-166
0.5 mMhrp1p-17[U-100% 13C; U-100% 15N]6
0.5 mManchor RNA-186
Sample conditionsIonic strength: 160 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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