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- PDB-3q2s: Crystal Structure of CFIm68 RRM/CFIm25 complex -

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Basic information

Entry
Database: PDB / ID: 3q2s
TitleCrystal Structure of CFIm68 RRM/CFIm25 complex
Components
  • Cleavage and polyadenylation specificity factor subunit 5
  • Cleavage and polyadenylation specificity factor subunit 6
KeywordsNUCLEAR PROTEIN / CFIm / CFIm25 / CFIm68 / CPSF5 / CPSF6 / CPSF / 3' end processing / RNA processing / cleavage factor / Nudix protein / protein-protein complex / RRM domain / nudix fold / RNA
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 / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation ...exon-exon junction complex binding / positive regulation of pro-B cell differentiation / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / positive regulation of stem cell differentiation / mRNA 3'-UTR AU-rich region binding / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / mRNA 3'-end processing / paraspeckles / RNA Polymerase II Transcription Termination / post-transcriptional regulation of gene expression / protein heterotetramerization / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / Signaling by FGFR1 in disease / protein tetramerization / centriolar satellite / histone deacetylase binding / mRNA processing / cell differentiation / nuclear speck / nuclear body / ribonucleoprotein complex / mRNA binding / centrosome / chromatin binding / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsYang, Q. / Coseno, M. / Gilmartin, G.M. / Doublie, S.
CitationJournal: Structure / Year: 2011
Title: Crystal Structure of a Human Cleavage Factor CFI(m)25/CFI(m)68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping.
Authors: Yang, Q. / Coseno, M. / Gilmartin, G.M. / Doublie, S.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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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 6
D: Cleavage and polyadenylation specificity factor subunit 6


Theoretical massNumber of molelcules
Total (without water)97,0334
Polymers97,0334
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-32 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.323, 139.323, 139.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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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 / Nucleoside ...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: 24030.703 Da / Num. of mol.: 2 / Fragment: residues 21-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFIM25, CPSF25, CPSF5, NUDT21, or CPSF5 / Plasmid: His6-MBP fusion vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: O43809
#2: Protein Cleavage and polyadenylation specificity factor subunit 6 / Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 24485.863 Da / Num. of mol.: 2 / Fragment: RRM domain, residues 13-235 / Mutation: C159V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFIM68, CPSF6 / Plasmid: pET22 C-terminal His6 tag / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q16630
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2M Magnesium Formate, 0.05M HEPES pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 23, 2010 / Details: mirrors
RadiationMonochromator: MAR mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.04
ReflectionResolution: 2.9→20 Å / Num. all: 20194 / Num. obs: 20194 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 16.7 % / Num. unique all: 1968 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å46.34 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BHO

3bho


Resolution: 2.9→19.903 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7745
Cross valid method: Throughout. Twin based reflections are in the same set
σ(F): 0.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 1804 5.67 %Random
Rwork0.2126 ---
obs0.2153 20194 82.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.751 Å2 / ksol: 0.245 e/Å3
Displacement parametersBiso max: 137.05 Å2 / Biso mean: 64.8149 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 0 20 4843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054966
X-RAY DIFFRACTIONf_angle_d0.9436739
X-RAY DIFFRACTIONf_chiral_restr0.061733
X-RAY DIFFRACTIONf_plane_restr0.004871
X-RAY DIFFRACTIONf_dihedral_angle_d17.1791852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9013-2.99460.39031170.34052110222760
2.9946-3.10130.41611210.31272251237264
3.1013-3.22490.31721240.30042421254570
3.2249-3.3710.41041070.2622722282978
3.371-3.54770.35921350.24612617275275
3.5477-3.76850.32291510.25142977312885
3.7685-4.0570.261390.20252771291079
4.057-4.46090.30111700.17832959312984
4.4609-5.09630.20821540.16363039319387
5.0963-6.38320.281620.20723103326588
6.3832-19.50960.22011880.1853243343192

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