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- PDB-3n9u: Crystal Structure of the Complex between the 25 kDa Subunit and t... -

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Basic information

Entry
Database: PDB / ID: 3n9u
TitleCrystal Structure of the Complex between the 25 kDa Subunit and the 59 kDa Subunit (RRM domain) of Human Cleavage Factor Im
Components
  • Cleavage and polyadenylation specificity factor subunit 5
  • Cleavage and polyadenylation specificity factor subunit 7
KeywordsSPLICING / Protein-protein complex / Coexpression / Heterotetramer / mRNA maturation / polyadenylation / mRNA cleavage / cleavage and polyadenylation specificity factor subunit 5 / cleavage and polyadenylation specificity factor subunit 7 / pre-mRNA cleavage factor Im 25 kDa subunit / pre-mRNA cleavage factor Im 59 kDa subunit / NUDIX / hydrolase / RRM domain / NUDT21 / CPSF5 / CPSF7 / Structural Genomics / Structural Genomics Consortium / SGC / SGC Stockholm
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 ...: / 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 / RNA Polymerase II Transcription Termination / protein heterotetramerization / post-transcriptional regulation of gene expression / termination of RNA polymerase II transcription / : / Processing of Capped Intron-Containing Pre-mRNA / centriolar satellite / mRNA Splicing - Major Pathway / protein tetramerization / mRNA processing / histone deacetylase binding / mRNA splicing, via spliceosome / cell differentiation / nuclear body / 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 7 / CPSF7, RNA recognition motif / 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 ...Cleavage and polyadenylation specificity factor subunit 7 / CPSF7, RNA recognition motif / 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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Moche, M. / Nielsen, T.N. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the Complex between the 25 kDa Subunit and the 59 kDa Subunit (RRM domain) of Human Cleavage Factor Im
Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / ...Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P.
History
DepositionMay 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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 7
I: Cleavage and polyadenylation specificity factor subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1407
Polymers88,8634
Non-polymers2763
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-33 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.950, 124.730, 40.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 26720.654 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: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE / References: UniProt: O43809
#2: Protein Cleavage and polyadenylation specificity factor subunit 7 / / Cleavage and polyadenylation specificity factor 59 kDa subunit / CPSF 59 kDa subunit / Pre-mRNA ...Cleavage and polyadenylation specificity factor 59 kDa subunit / CPSF 59 kDa subunit / Pre-mRNA cleavage factor Im 59 kDa subunit


Mass: 17711.008 Da / Num. of mol.: 2 / Fragment: RRM domain, residues 50-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF7 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE / References: UniProt: Q8N684
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 20% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.92→55.317 Å / Num. all: 64843 / Num. obs: 63481 / % possible obs: 97.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.038 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 8
Reflection shellResolution: 1.92→2.029 Å / Redundancy: 4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9250 / Rsym value: 0.438 / % possible all: 94

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CL3

2cl3


Resolution: 1.92→40.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.153 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23134 3216 5.1 %RANDOM
Rwork0.19601 ---
obs0.1978 60194 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---1.36 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.92→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4763 0 18 417 5198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224915
X-RAY DIFFRACTIONr_bond_other_d0.0010.023406
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9726673
X-RAY DIFFRACTIONr_angle_other_deg0.86638312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38924.236229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91515851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2021529
X-RAY DIFFRACTIONr_chiral_restr0.0860.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02976
X-RAY DIFFRACTIONr_mcbond_it0.941.52959
X-RAY DIFFRACTIONr_mcbond_other0.2121.51180
X-RAY DIFFRACTIONr_mcangle_it1.69724809
X-RAY DIFFRACTIONr_scbond_it2.25931956
X-RAY DIFFRACTIONr_scangle_it3.7174.51860
LS refinement shellResolution: 1.92→1.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 195 -
Rwork0.301 4027 -
obs--90.37 %

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