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- PDB-4jxt: CID of human RPRD1A in complex with a phosphorylated peptide from... -

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Basic information

Entry
Database: PDB / ID: 4jxt
TitleCID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD
Components
  • DNA-directed RNA polymerase II subunit RPB1
  • Regulation of nuclear pre-mRNA domain-containing protein 1A
KeywordsPROTEIN BINDING / Structural Genomics Consortium / Structural Genomics / SGC
Function / homology
Function and homology information


microfibril binding / RNA polymerase II promoter clearance / mRNA 3'-end processing / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / transcription preinitiation complex / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection ...microfibril binding / RNA polymerase II promoter clearance / mRNA 3'-end processing / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / transcription preinitiation complex / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / 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 / mRNA Splicing - Minor Pathway / RNA polymerase II complex binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II C-terminal domain binding / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / 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 / RNA polymerase II activity / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / DNA-templated transcription termination / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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-dependent RNA polymerase activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Regulation of nuclear pre-mRNA domain-containing protein 1A/B / Cell-cycle alteration and expression-elevated protein in tumour / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA polymerase II, heptapeptide repeat, eukaryotic ...: / Regulation of nuclear pre-mRNA domain-containing protein 1A/B / Cell-cycle alteration and expression-elevated protein in tumour / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / 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 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / Regulation of nuclear pre-mRNA domain-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsNi, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Greenblatt, J.F. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.
Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El ...Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El Bakkouri, M. / Senisterra, G.A. / He, H. / Huang, H. / Sidhu, S.S. / Emili, A. / Murphy, S. / Mosley, A.L. / Arrowsmith, C.H. / Min, J. / Greenblatt, J.F.
History
DepositionMar 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulation of nuclear pre-mRNA domain-containing protein 1A
B: DNA-directed RNA polymerase II subunit RPB1


Theoretical massNumber of molelcules
Total (without water)18,5078
Polymers18,5072
Non-polymers06
Water1,56787
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.264, 93.264, 36.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Regulation of nuclear pre-mRNA domain-containing protein 1A / Cyclin-dependent kinase inhibitor 2B-related protein / p15INK4B-related protein


Mass: 16063.418 Da / Num. of mol.: 1 / Fragment: UNP residues 1-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD1A, P15RS / Plasmid: pET15 MHL / Strain (production host): BL 21 / References: UniProt: Q96P16
#2: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


Mass: 2443.259 Da / Num. of mol.: 1 / Fragment: UNP residues 1612-1630 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human)
References: UniProt: P24928, DNA-directed RNA polymerase, RNA-directed RNA polymerase
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBIOTIN (BTN) IS LINKED TO THE N TERMINUS OF THE SHORT PEPTIDE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG-4000, 10% isopropanol, 0.1M HEPES., pH 7.5, vapor diffusion, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
XDSdataset1001
11
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 12196 / % possible obs: 98.26 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.7596
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.9-27.20.93123201711196.34
2-2.127.30.55121431664197.29
2.12-2.277.330.36114871568197.86
2.27-2.457.340.28107071458198.39
2.45-2.697.370.1799691353198.77
2.69-37.340.1291141242198.58
3-3.477.370.0781101101199.72
3.47-4.257.320.056894942199.64
4.25-6.017.240.045337737199.93
6.01-3070.032939420199.11

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9data scaling
PHASERphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HFG

4hfg


Resolution: 1.9→29.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.685 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED difference electron density for the Y1629 residue of the peptide ligand suggests an alternative interpretation of ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED difference electron density for the Y1629 residue of the peptide ligand suggests an alternative interpretation of the electron density in this area. It is possible that that the peptide's main chain continues where the Y1629 side chain is currently modeled. Electron density suggests covalent modification of CYS-100. ARP/WARP, COOT, the moloprobity server were also used during refinement of the model.
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 590 4.838 %RANDOM
Rwork0.1843 ---
obs0.187 12195 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 58.53 Å2 / Biso mean: 23.393 Å2 / Biso min: 11.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.127 Å20 Å20 Å2
2--0.127 Å20 Å2
3----0.254 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 6 87 1225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021216
X-RAY DIFFRACTIONr_bond_other_d0.0010.021134
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9631658
X-RAY DIFFRACTIONr_angle_other_deg0.86132627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67724.10756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4315216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.862157
X-RAY DIFFRACTIONr_chiral_restr0.080.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211336
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9490.296330.28982787798.062
1.949-2.0020.304510.24179589394.737
2.002-2.060.297380.21780684799.646
2.06-2.1230.22410.19175984295.012
2.123-2.1930.217430.196758801100
2.193-2.2690.231290.19273379695.729
2.269-2.3540.305370.20772075999.736
2.354-2.450.285360.18367773497.139
2.45-2.5580.283420.17764069298.555
2.558-2.6820.241340.17862666798.951
2.682-2.8250.229230.17761464798.454
2.825-2.9950.236310.18756460099.167
2.995-3.20.198210.19155658099.483
3.2-3.4530.297280.18750753899.442
3.453-3.7770.246230.17846048699.383
3.777-4.2150.159210.14543745999.782
4.215-4.8510.144180.1438039999.749
4.851-5.9030.242190.166329348100
5.903-8.1910.205110.18925827099.63
8.191-300.199110.18615917298.837
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8320.46090.7982.5971.44883.82510.033-0.14360.04490.0102-0.0561-0.1554-0.2020.01680.02310.01950.0005-0.01140.0306-0.00010.03823.95024.5692-0.1057
212.6328-0.8429-8.68072.46415.026614.1887-0.5077-0.15610.5028-0.6558-0.2590.5404-0.8708-0.45150.76680.33250.1328-0.14160.0542-0.06440.175414.104912.244-3.44
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 132
2X-RAY DIFFRACTION2B1620 - 1630

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