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- PDB-3q2t: Crystal Structure of CFIm68 RRM/CFIm25/RNA complex -

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Basic information

Entry
Database: PDB / ID: 3q2t
TitleCrystal Structure of CFIm68 RRM/CFIm25/RNA complex
Components
  • Cleavage and polyadenylation specificity factor subunit 5
  • Cleavage and polyadenylation specificity factor subunit 6
  • RNA
KeywordsRNA BINDING PROTEIN/RNA / CFIm / CFIm25 / CFIm68 / CPSF5 / CPSF6 / CPSF / 3' end processing / RNA processing / cleavage factor / Nudix protein / protein-protein complex / protein-RNA complex / RRM / nudix fold / RNA BINDING PROTEIN-RNA complex
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 / protein heterotetramerization / RNA Polymerase II Transcription Termination / 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
RNA / 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: 3.061 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

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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
E: RNA
F: RNA


Theoretical massNumber of molelcules
Total (without water)100,1296
Polymers100,1296
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.406, 138.406, 138.406
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 / 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: RNA chain RNA /


Mass: 1547.952 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized by Dharmacon
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
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: Mar 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: 0.033
ReflectionResolution: 3.06→20 Å / Num. all: 16919 / Num. obs: 16919 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 36.8 % / Rmerge(I) obs: 0.146 / Χ2: 0.998 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.06-3.1727.50.999916341.024100
3.17-3.330.80.92616861.001100
3.3-3.4432.60.6116791100
3.44-3.6334.20.47516700.998100
3.63-3.8535.70.35816831.005100
3.85-4.15370.21616780.992100
4.15-4.5638.50.15816871.002100
4.56-5.2141.30.1091696199.9
5.21-6.5244.80.11217220.996100
6.52-2044.40.05317840.978100

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Phasing

PhasingMethod: molecular replacement

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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: 3.061→19.977 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.786
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
Rfree0.2858 1548 5.67 %Random
Rwork0.2108 ---
obs0.2137 16919 84.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.161 Å2 / ksol: 0.233 e/Å3
Displacement parametersBiso max: 153.66 Å2 / Biso mean: 64.4604 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: 3.061→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 204 0 3 5025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065178
X-RAY DIFFRACTIONf_angle_d0.9667064
X-RAY DIFFRACTIONf_chiral_restr0.059776
X-RAY DIFFRACTIONf_plane_restr0.003880
X-RAY DIFFRACTIONf_dihedral_angle_d17.4481958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.061-3.18260.50411150.29562263237864
3.1826-3.32680.32341540.27612922307680
3.3268-3.50120.34461590.25942881304081
3.5012-3.7190.36171520.24172875302780
3.719-4.00380.33881360.20972738287478
4.0038-4.40230.27931510.18142928307981
4.4023-5.02930.21741530.1772961311483
5.0293-6.29890.30651520.20953083323586
6.2989-19.19380.22521830.19113270345392

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