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- PDB-4q96: CID of human RPRD1B in complex with an unmodified CTD peptide -

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Basic information

Entry
Database: PDB / ID: 4q96
TitleCID of human RPRD1B in complex with an unmodified CTD peptide
Components
  • RPB1-CTD
  • Regulation of nuclear pre-mRNA domain-containing protein 1B
KeywordsPROTEIN BINDING / transcription / 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. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / 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 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references

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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: Regulation of nuclear pre-mRNA domain-containing protein 1B
E: Regulation of nuclear pre-mRNA domain-containing protein 1B
F: RPB1-CTD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,03433
Polymers66,6496
Non-polymers38427
Water4,089227
1
D: Regulation of nuclear pre-mRNA domain-containing protein 1B
E: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,41018
Polymers31,1212
Non-polymers28816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-30 kcal/mol
Surface area13300 Å2
MethodPISA
2
A: Regulation of nuclear pre-mRNA domain-containing protein 1B
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,21712
Polymers31,1212
Non-polymers9610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-29 kcal/mol
Surface area13500 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-84 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.653, 134.707, 55.706
Angle α, β, γ (deg.)90.000, 106.640, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
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): BL 21 / References: UniProt: Q9NQG5
#2: Protein/peptide RPB1-CTD


Mass: 2203.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 23 / Source method: obtained synthetically
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE VARIANT, AS LISTED IN UNIPROT ENTRY Q9NQG5

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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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG-1500, 0.2M ammonium sulfate, 0.1M HEPES, pH 7.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.848→67.353 Å / Num. all: 66812 / Num. obs: 66812 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.089 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.953.80.8510.93677297110.851100
1.95-2.073.80.4671.73511492310.46799.9
2.07-2.213.80.2722.93288686310.27299.9
2.21-2.393.80.19543070880590.195100
2.39-2.623.80.1246.22822874180.124100
2.62-2.933.80.0918.52570467570.091100
2.93-3.383.80.05912.42226459130.059100
3.38-4.143.70.04316.21855950300.043100
4.14-5.853.70.037171433638960.037100
5.85-44.6543.60.03714.5770121660.03799.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→44.654 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.27 / σ(F): 1.01 / Phase error: 30.77 / Stereochemistry target values: ML
Details: xprep was used for the analysis of diffraction intensities. refmac, autobuster, molrep, coot, the molprobity server were also used during refinement. Some uninterpreted electron density ...Details: xprep was used for the analysis of diffraction intensities. refmac, autobuster, molrep, coot, the molprobity server were also used during refinement. Some uninterpreted electron density likely represents additional N-terminal residues of the CID construct, but fails to resolve a continuous trace of the protein chain. scaling of diffraction data in a c-centered orthorhombic setting with cell dimensions a, b, c = 66.5, 89.3, 134.8 Angstroms produced reasonable merging statistics, but model refinement progressed poorly in that setting. The L-test as implemented by PHENIX.XTRIAGE detected intensity statistics suggestive of twinning. Twin refinement was not pursued due to diminished map interpretability and poor comparability of R-factors, caveats cited in the PHENIX.XTRIAGE program output. We thank Huanwang Yang for helpful discussion.
RfactorNum. reflection% reflection
Rfree0.2709 2024 3.03 %
Rwork0.2378 64737 -
obs0.2389 66761 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.87 Å2 / Biso mean: 24.5097 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 43 227 4712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074659
X-RAY DIFFRACTIONf_angle_d1.0766304
X-RAY DIFFRACTIONf_chiral_restr0.041686
X-RAY DIFFRACTIONf_plane_restr0.006798
X-RAY DIFFRACTIONf_dihedral_angle_d13.6031762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.89630.403790.315847194728
1.8963-1.9475100000000.29994763
1.9475-2.00480.33184490.283743114760
2.0048-2.0696100000000.2684766
2.0696-2.1435100000000.25874799
2.1435-2.22930.29963210.240744144735
2.2293-2.3308100000000.24154743
2.3308-2.45370.28172650.245444774742
2.4537-2.60740.28852370.237645454782
2.6074-2.8087100000000.24824777
2.8087-3.09130.28711970.244645914788
3.0913-3.53840.27451520.22546104762
3.5384-4.45740.24582240.208145764800
4.4574-44.66730.22611700.217646464816

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