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- PDB-4q94: human RPRD1B CID in complex with a RPB1-CTD derived Ser2 phosphor... -

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Basic information

Entry
Database: PDB / ID: 4q94
Titlehuman RPRD1B CID in complex with a RPB1-CTD derived Ser2 phosphorylated peptide
Components
  • Regulation of nuclear pre-mRNA domain-containing protein 1B
  • rpb1-ctd
KeywordsPEPTIDE BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / transcription preinitiation complex / RNA polymerase II complex binding / RNA polymerase II C-terminal domain binding / RNA polymerase II transcribes snRNA genes / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / nucleoplasm ...regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / transcription preinitiation complex / RNA polymerase II complex binding / RNA polymerase II C-terminal domain binding / RNA polymerase II transcribes snRNA genes / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...: / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Regulation of nuclear pre-mRNA domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsNi, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Bountra, C. / 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
DepositionApr 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Sep 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 1B
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
C: rpb1-ctd
D: rpb1-ctd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,13626
Polymers35,8484
Non-polymers28822
Water1,47782
1
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
D: rpb1-ctd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,02012
Polymers17,9242
Non-polymers9610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-4 kcal/mol
Surface area8720 Å2
MethodPISA
2
A: Regulation of nuclear pre-mRNA domain-containing protein 1B
C: rpb1-ctd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,11614
Polymers17,9242
Non-polymers19212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area8780 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-39 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.286, 70.448, 108.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Regulation of nuclear pre-mRNA domain-containing protein 1B / Cell cycle-related and expression-elevated protein in tumor


Mass: 15560.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD1B, C20orf77, CREPT / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9NQG5
#2: Protein/peptide rpb1-ctd


Mass: 2363.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 2.0 M ammonium sulfate, 5% isopropanol, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→43.11 Å / Num. obs: 26622 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.85-1.897.31.0761.9117081612100
9.06-43.075.40.02453.5146827496.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4fld

4fld
PDB Unreleased entry


Resolution: 1.85→43.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2161 / WRfactor Rwork: 0.1704 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8488 / SU B: 2.997 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1294 / SU Rfree: 0.1274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1300 4.9 %THIN SHELLS (SFTOOLS)
Rwork0.1777 ---
obs0.1801 26564 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.35 Å2 / Biso mean: 31.8293 Å2 / Biso min: 16.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.33 Å2-0 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 34 82 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192322
X-RAY DIFFRACTIONr_bond_other_d0.0010.022155
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9583155
X-RAY DIFFRACTIONr_angle_other_deg0.8943.0014956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7025290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02522.82899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60415393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2151516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 16 -
Rwork0.264 1904 -
all-1920 -
obs--99.95 %

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