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- PDB-32pv: human CSTF50 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 32pv
Titlehuman CSTF50 N-terminal domain
ComponentsCleavage stimulation factor subunit 1
KeywordsNUCLEAR PROTEIN / RNA processing factor
Function / homology
Function and homology information


mRNA cleavage stimulating factor complex / Processing of Intronless Pre-mRNAs / mRNA 3'-end processing / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / RNA binding / nucleoplasm
Similarity search - Function
Cleavage stimulation factor subunit 1, dimerisation domain / CSTF1, dimerization domain superfamily / Cleavage stimulation factor subunit 1-like / Cleavage stimulation factor subunit 1, dimerisation domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...Cleavage stimulation factor subunit 1, dimerisation domain / CSTF1, dimerization domain superfamily / Cleavage stimulation factor subunit 1-like / Cleavage stimulation factor subunit 1, dimerisation domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cleavage stimulation factor subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsEnnis-Adeniran, V. / Purkiss, A.G. / Taylor, I.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome TrustCC2029 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2029 United Kingdom
Cancer Research UKCC2029 United Kingdom
CitationJournal: To Be Published
Title: human CSTF50 N-terminal domain
Authors: Ennis-Adeniran, V. / Purkiss, A.G. / Taylor, I.A.
History
DepositionJul 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cleavage stimulation factor subunit 1
B: Cleavage stimulation factor subunit 1
C: Cleavage stimulation factor subunit 1
D: Cleavage stimulation factor subunit 1
E: Cleavage stimulation factor subunit 1
F: Cleavage stimulation factor subunit 1


Theoretical massNumber of molelcules
Total (without water)47,4316
Polymers47,4316
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Solution oligomer is a dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.759, 65.591, 160.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Cleavage stimulation factor subunit 1 / CF-1 50 kDa subunit / Cleavage stimulation factor 50 kDa subunit / CSTF 50 kDa subunit / CstF-50


Mass: 7905.176 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05048
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG3350, 0.2 M NaCl, 0.1 M Na-HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→80.26 Å / Num. obs: 54800 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.061 / Net I/σ(I): 14.5
Reflection shellResolution: 1.56→1.65 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 50580 / CC1/2: 0.833 / Rpim(I) all: 0.273 / Rrim(I) all: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→60.72 Å / SU ML: 0.1891 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 2808 5.13 %
Rwork0.2015 51904 -
obs0.203 54712 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.58 Å2
Refinement stepCycle: LAST / Resolution: 1.56→60.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 0 177 2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01162813
X-RAY DIFFRACTIONf_angle_d1.15273813
X-RAY DIFFRACTIONf_chiral_restr0.0697447
X-RAY DIFFRACTIONf_plane_restr0.008491
X-RAY DIFFRACTIONf_dihedral_angle_d16.59551079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.590.31831210.27412518X-RAY DIFFRACTION99.89
1.59-1.620.31241420.24492573X-RAY DIFFRACTION100
1.62-1.650.28811410.232538X-RAY DIFFRACTION99.96
1.65-1.680.22941280.22152577X-RAY DIFFRACTION100
1.68-1.720.2321330.21182557X-RAY DIFFRACTION99.96
1.72-1.760.24741470.2182540X-RAY DIFFRACTION99.96
1.76-1.80.25491420.2222580X-RAY DIFFRACTION99.96
1.8-1.850.27671380.24382554X-RAY DIFFRACTION100
1.85-1.910.27621510.23382586X-RAY DIFFRACTION99.96
1.91-1.970.27391440.20852563X-RAY DIFFRACTION100
1.97-2.040.24481470.20822556X-RAY DIFFRACTION99.96
2.04-2.120.21051320.18912613X-RAY DIFFRACTION99.89
2.12-2.220.23611440.18652581X-RAY DIFFRACTION100
2.22-2.330.22351640.18772559X-RAY DIFFRACTION100
2.33-2.480.21591250.19562600X-RAY DIFFRACTION100
2.48-2.670.19491290.20012639X-RAY DIFFRACTION99.93
2.67-2.940.23071530.20282606X-RAY DIFFRACTION99.93
2.94-3.360.22531390.19662650X-RAY DIFFRACTION99.89
3.36-4.240.22511430.18362675X-RAY DIFFRACTION99.75
4.24-60.720.21941450.20592839X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: -8.40867966461 Å / Origin y: -5.38750338517 Å / Origin z: -18.5084357034 Å
111213212223313233
T0.166834129496 Å2-0.0239781774795 Å2-0.0194895426828 Å2-0.19818298785 Å20.0129031160154 Å2--0.200094283326 Å2
L0.213988625566 °2-0.0405796605458 °2-0.0420842960579 °2-0.102294832214 °20.131540403521 °2--0.639611193549 °2
S-0.0446628906772 Å °0.0812033501645 Å °0.0333240332146 Å °-0.0433725776618 Å °0.0137079457407 Å °-0.00547206479565 Å °-0.068382109667 Å °0.0509297710357 Å °0.0259952130532 Å °
Refinement TLS groupSelection details: all

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