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- PDB-3bho: Crystal Structure of the 25kDa Subunit of Human Cleavage factor I... -

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Basic information

Entry
Database: PDB / ID: 3bho
TitleCrystal Structure of the 25kDa Subunit of Human Cleavage factor Im with Ap4A
ComponentsCleavage and polyadenylation specificity factor subunit 5
KeywordsNUCLEAR PROTEIN / CPSF5 / RNA processing / cleavage factor / diadenosine tetraphosphate / mRNA processing / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


positive regulation of pro-B cell differentiation / : / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-UTR AU-rich region binding / paraspeckles / mRNA 3'-end processing ...positive regulation of pro-B cell differentiation / : / mRNA cleavage factor complex / Processing of Intronless Pre-mRNAs / positive regulation of stem cell differentiation / 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 / protein heterotetramerization / RNA Polymerase II Transcription Termination / post-transcriptional regulation of gene expression / : / Processing of Capped Intron-Containing Pre-mRNA / centriolar satellite / protein tetramerization / mRNA processing / histone deacetylase binding / cell differentiation / nuclear body / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cleavage/polyadenylation specificity factor subunit 5 / Nucleotide hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Cleavage and polyadenylation specificity factor subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 1.8 Å
AuthorsCoseno, M. / Doublie, S.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Crystal structure of the 25 kDa subunit of human cleavage factor Im.
Authors: Coseno, M. / Martin, G. / Berger, C. / Gilmartin, G. / Keller, W. / Doublie, S.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0142
Polymers24,1781
Non-polymers8361
Water3,063170
1
A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules

A: Cleavage and polyadenylation specificity factor subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0294
Polymers48,3562
Non-polymers1,6732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.955, 79.955, 72.186
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 24177.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT21, CFIM25, CPSF25, CPSF5 / Plasmid: His6-MBP fusion vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: O43809
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ap4A


Mass: 836.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 0.025M Magnesium chloride, 0.1M Tris-HCL pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.54
SYNCHROTRONNSLS X12B21
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEDec 9, 2006mirrors
ADSC QUANTUM 42CCDJan 10, 2007mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
211
ReflectionRedundancy: 10.1 % / Av σ(I) over netI: 14.9 / Number: 254045 / Rmerge(I) obs: 0.041 / Χ2: 1.04 / D res high: 1.75 Å / D res low: 20 Å / Num. obs: 25175 / % possible obs: 91.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.762099.610.031.2639.9
2.993.7610010.0341.25610.5
2.612.9910010.0441.1310.6
2.372.6110010.0541.01610.7
2.22.3710010.071.02310.7
2.072.210010.0890.9610.7
1.972.0710010.1270.92310.6
1.891.9710010.1760.90610.6
1.811.8999.710.2390.8427.5
1.751.8119.110.2990.8075.5
ReflectionResolution: 1.8→15 Å / Num. all: 47788 / Num. obs: 46800 / % possible obs: 97.9 % / Redundancy: 21.6 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 66
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2454

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Isomorphous Replacement
Starting model: 3BAP

3bap


Resolution: 1.8→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4580 9.6 %10%
Rwork0.202 ---
obs-46800 97.9 %-
Solvent computationBsol: 50.046 Å2
Displacement parametersBiso mean: 34.322 Å2
Baniso -1Baniso -2Baniso -3
1-2.038 Å2-0.052 Å20 Å2
2--2.038 Å20 Å2
3----4.076 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 22 170 1833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.269
X-RAY DIFFRACTIONc_mcbond_it1.4261.5
X-RAY DIFFRACTIONc_scbond_it2.0932
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scangle_it3.2222.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2dna-rna_rep-040219mr.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5hetero-cpds-060110mr.parhetero-cpds-070507mcC.top

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