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- PDB-9hm8: NMR solution structure of RPRD2 CTD-interacting domain and pS2,7 ... -

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Basic information

Entry
Database: PDB / ID: 9hm8
TitleNMR solution structure of RPRD2 CTD-interacting domain and pS2,7 RNAPII CTD peptide.
Components
  • DNA-directed RNA polymerase II subunit RPB1
  • Regulation of nuclear pre-mRNA domain-containing protein 2
KeywordsPROTEIN BINDING / RPRD2 / CID / RNAPII / CTD / Complex
Function / homology
Function and homology information


microfibril binding / mRNA 3'-end processing / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription preinitiation complex / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE ...microfibril binding / mRNA 3'-end processing / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription preinitiation complex / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / RNA polymerase II C-terminal domain binding / RNA polymerase II complex binding / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / Inhibition of DNA recombination at telomere / positive regulation of RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / DNA-templated transcription termination / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / kinase binding / Formation of TC-NER Pre-Incision Complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-directed RNA polymerase activity / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / transcription by RNA polymerase II / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 ...: / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / Regulation of nuclear pre-mRNA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLinhartova, K. / Macosek, J. / Kubicek, K. / Smirakova, E. / Stefl, R.
Funding supportEuropean Union, Czech Republic, 3items
OrganizationGrant numberCountry
European Research Council (ERC)649030European Union
Czech Science FoundationGA22-19896S Czech Republic
Ministry of Education (MoE, Czech Republic)CZ.02.01.01/00/22_008/0004575 Czech Republic
CitationJournal: To Be Published
Title: NMR solution structure of RPRD2 CTD-interacting domain and pS2,7 RNAPII CTD peptide.
Authors: Linhartova, K. / Macosek, J. / Kubicek, K. / Smirakova, E. / Steel, R.
History
DepositionDec 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulation of nuclear pre-mRNA domain-containing protein 2
B: DNA-directed RNA polymerase II subunit RPB1


Theoretical massNumber of molelcules
Total (without water)18,7182
Polymers18,7182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence anisotropy mutagenesis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1first structure in the bundle

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Components

#1: Protein Regulation of nuclear pre-mRNA domain-containing protein 2


Mass: 17305.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD2, KIAA0460, HSPC099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5VT52
#2: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II subunit A / ...RNA polymerase II subunit B1 / 3'-5' exoribonuclease / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


Mass: 1412.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P24928, DNA-directed RNA polymerase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, RNA-directed RNA polymerase
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
132isotropic32D 1H-13C HSQC aliphatic
142isotropic32D 1H-13C HSQC aromatic
1112isotropic12D 1H-15N HSQC
152isotropic33D 1H-13C NOESY aliphatic
162isotropic33D 1H-13C NOESY aromatic
182isotropic33D 1H-15N NOESY
112isotropic23D (H)CC(CO)NH
1122isotropic13D HNCA
172isotropic13D HN(CA)CB
192isotropic13D CBCA(CO)NH
1102isotropic33D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1 mM pS2pS7 CTD, 90% H2O/10% D2O
Label: RPRD2-pS2pS7 CTD / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMRPRD2 CID[U-100% 13C; U-100% 15N]2
1 mMpS2pS7 CTDnone2
Sample conditionsDetails: 50 mM Tris, 100 mM NaCl, 10 mM beta-merkaptoethanol
Ionic strength: 100 mM / Label: NMR buffer / pH: 8 / Pressure: 1 Pa / Temperature: 293.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD8501
Bruker AVANCE III HDBrukerAVANCE III HD7002
Bruker AVANCE III HDBrukerAVANCE III HD9503

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.8/v10 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: first structure in the bundle
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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