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- PDB-3p5t: CFIm25-CFIm68 complex -

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Basic information

Entry
Database: PDB / ID: 3p5t
TitleCFIm25-CFIm68 complex
Components
  • Cleavage and polyadenylation specificity factor subunit 5
  • Cleavage and polyadenylation specificity factor subunit 6
KeywordsRNA BINDING PROTEIN / RRM domain / Poly(A) site recognition / RNA / nuclear
Function / homology
Function and homology information


exon-exon junction complex binding / positive regulation of pro-B cell differentiation / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex ...exon-exon junction complex binding / positive regulation of pro-B cell differentiation / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-UTR AU-rich region binding / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / RNA Polymerase II Transcription Termination / protein heterotetramerization / post-transcriptional regulation of gene expression / : / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / centriolar satellite / localization / Signaling by FGFR1 in disease / protein tetramerization / mRNA processing / histone deacetylase binding / cell differentiation / nuclear body / nuclear speck / ribonucleoprotein complex / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / RRM (RNA recognition motif) domain / NUDIX hydrolase-like domain superfamily ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / RRM (RNA recognition motif) domain / NUDIX hydrolase-like domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cleavage and polyadenylation specificity factor subunit 5 / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, H. / Tong, S. / Li, X. / Shi, H. / Gao, Y. / Ge, H. / Niu, L. / Teng, M.
CitationJournal: To be Published
Title: Structural basis of pre-mRNA recognition by the human cleavage factor Im complex
Authors: Li, H. / Tong, S. / Li, X. / Shi, H. / Gao, Y. / Ge, H. / Niu, L. / Teng, M.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 5
B: Cleavage and polyadenylation specificity factor subunit 5
C: Cleavage and polyadenylation specificity factor subunit 5
D: Cleavage and polyadenylation specificity factor subunit 5
E: Cleavage and polyadenylation specificity factor subunit 5
F: Cleavage and polyadenylation specificity factor subunit 5
L: Cleavage and polyadenylation specificity factor subunit 6
M: Cleavage and polyadenylation specificity factor subunit 6
N: Cleavage and polyadenylation specificity factor subunit 6
O: Cleavage and polyadenylation specificity factor subunit 6
P: Cleavage and polyadenylation specificity factor subunit 6
Q: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)202,58112
Polymers202,58112
Non-polymers00
Water4,468248
1
A: Cleavage and polyadenylation specificity factor subunit 5
B: Cleavage and polyadenylation specificity factor subunit 5
L: Cleavage and polyadenylation specificity factor subunit 6
M: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers67,5274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cleavage and polyadenylation specificity factor subunit 5
D: Cleavage and polyadenylation specificity factor subunit 5
N: Cleavage and polyadenylation specificity factor subunit 6
O: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers67,5274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cleavage and polyadenylation specificity factor subunit 5
F: Cleavage and polyadenylation specificity factor subunit 5
P: Cleavage and polyadenylation specificity factor subunit 6
Q: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)67,5274
Polymers67,5274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.440, 105.690, 147.080
Angle α, β, γ (deg.)90.00, 112.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cleavage and polyadenylation specificity factor subunit 5 / / Cleavage factor Im 25 / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 ...Cleavage factor Im 25 / Cleavage and polyadenylation specificity factor 25 kDa subunit / CPSF 25 kDa subunit / Nucleoside diphosphate-linked moiety X motif 21 / Nudix motif 21 / Pre-mRNA cleavage factor Im 25 kDa subunit


Mass: 23614.115 Da / Num. of mol.: 6 / Fragment: UNP residues 34-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT21, CFIM25, CPSF25, CPSF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O43809
#2: Protein
Cleavage and polyadenylation specificity factor subunit 6 / / Cleavage factor Im 68 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CF Im68 / ...Cleavage factor Im 68 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CF Im68 / CPSF 68 kDa subunit / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 10149.415 Da / Num. of mol.: 6 / Fragment: UNP residues 80-161 / Mutation: C159S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF6, CFIM68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16630
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% PEG 3350, 5% dioxane, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 3, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 62054 / Num. obs: 58226 / % possible obs: 98.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.768 Å / % possible all: 98.92

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.4.0067refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CL3, 2FY1

2cl3

2fy1


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26543 3101 5.1 %RANDOM
Rwork0.21369 ---
all0.22 62054 --
obs0.21632 58226 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.363 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å2-1.44 Å2
2---2.32 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13005 0 0 248 13253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213354
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.96618188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0651639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2924.149605
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.796152117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5461567
X-RAY DIFFRACTIONr_chiral_restr0.0940.22008
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110259
X-RAY DIFFRACTIONr_mcbond_it0.5351.58246
X-RAY DIFFRACTIONr_mcangle_it0.994213262
X-RAY DIFFRACTIONr_scbond_it1.02135108
X-RAY DIFFRACTIONr_scangle_it1.8024.54926
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 227 -
Rwork0.362 4208 -
obs--99.35 %

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