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- PDB-6gx9: Crystal structure of the TNPO3 - CPSF6 RSLD complex -

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Basic information

Entry
Database: PDB / ID: 6gx9
TitleCrystal structure of the TNPO3 - CPSF6 RSLD complex
Components
  • Cleavage and polyadenylation specificity factor subunit 6
  • Transportin-3
KeywordsNUCLEAR PROTEIN / karyopherin-cargo complex / nuclear import / SR-like domain
Function / homology
Function and homology information


exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / annulate lamellae / 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 RNA export from nucleus / mRNA cleavage factor complex / annulate lamellae / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / RNA Polymerase II Transcription Termination / protein heterotetramerization / nuclear import signal receptor activity / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / localization / Signaling by FGFR1 in disease / protein tetramerization / mRNA processing / small GTPase binding / protein import into nucleus / nuclear envelope / nuclear speck / ribonucleoprotein complex / mRNA binding / intracellular membrane-bounded organelle / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Exportin-1/Importin-beta-like / Exportin 1-like protein / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Exportin-1/Importin-beta-like / Exportin 1-like protein / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
BENZAMIDINE / Cleavage and polyadenylation specificity factor subunit 6 / Transportin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCherepanov, P. / Cook, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)GM082251 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6.
Authors: Jang, S. / Cook, N.J. / Pye, V.E. / Bedwell, G.J. / Dudek, A.M. / Singh, P.K. / Cherepanov, P. / Engelman, A.N.
History
DepositionJun 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 22, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transportin-3
B: Transportin-3
C: Cleavage and polyadenylation specificity factor subunit 6
D: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,92012
Polymers227,2564
Non-polymers6648
Water54030
1
A: Transportin-3
C: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9606
Polymers113,6282
Non-polymers3324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-3 kcal/mol
Surface area40540 Å2
MethodPISA
2
B: Transportin-3
D: Cleavage and polyadenylation specificity factor subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9606
Polymers113,6282
Non-polymers3324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-3 kcal/mol
Surface area40730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.335, 200.335, 234.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Transportin-3 / / Importin-12 / Imp12 / Transportin-SR / TRN-SR


Mass: 104313.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO3, IPO12 / Plasmid: pETSUMO-TNPO3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5L0
#2: Protein Cleavage and polyadenylation specificity factor subunit 6 / / Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Cleavage ...Cleavage and polyadenylation specificity factor 68 kDa subunit / CPSF 68 kDa subunit / Cleavage factor Im complex 68 kDa subunit / CFIm68 / Pre-mRNA cleavage factor Im 68 kDa subunit / Protein HPBRII-4/7


Mass: 9314.888 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 38 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12.8% PEG MME 500, 6.4% PEG 20,000, 4% 1,6-hexandiol, 1.5% benzamidine, 75 mM NaCl, 40 mM MgCl2, 6 mM DTT, 80 mM Tris-bicine, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→50.69 Å / Num. obs: 76497 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 65.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.051 / Rrim(I) all: 0.179 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 12 % / Rmerge(I) obs: 1.931 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10987 / CC1/2: 0.422 / Rpim(I) all: 0.579 / Rrim(I) all: 2.018 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C0O

4c0o


Resolution: 2.7→50.646 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.02
RfactorNum. reflection% reflection
Rfree0.248 3194 4.18 %
Rwork0.2137 --
obs0.2152 76443 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→50.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14593 0 44 30 14667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214919
X-RAY DIFFRACTIONf_angle_d0.43220250
X-RAY DIFFRACTIONf_dihedral_angle_d11.7989038
X-RAY DIFFRACTIONf_chiral_restr0.0352364
X-RAY DIFFRACTIONf_plane_restr0.0032591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74030.32641190.29463139X-RAY DIFFRACTION100
2.7403-2.78310.29771280.29343167X-RAY DIFFRACTION100
2.7831-2.82870.38231540.31163101X-RAY DIFFRACTION100
2.8287-2.87750.33961150.32223137X-RAY DIFFRACTION100
2.8775-2.92980.36821420.30533146X-RAY DIFFRACTION100
2.9298-2.98620.29111400.29093140X-RAY DIFFRACTION100
2.9862-3.04710.34671380.28363143X-RAY DIFFRACTION100
3.0471-3.11340.32891260.27673153X-RAY DIFFRACTION100
3.1134-3.18580.29161400.27163149X-RAY DIFFRACTION100
3.1858-3.26540.28381390.25943136X-RAY DIFFRACTION100
3.2654-3.35370.3061410.25853165X-RAY DIFFRACTION100
3.3537-3.45240.35591400.26353156X-RAY DIFFRACTION100
3.4524-3.56380.28281380.24423142X-RAY DIFFRACTION100
3.5638-3.69110.27121410.2343177X-RAY DIFFRACTION100
3.6911-3.83890.28251410.21993176X-RAY DIFFRACTION100
3.8389-4.01350.22761410.19773174X-RAY DIFFRACTION100
4.0135-4.2250.21431410.18813185X-RAY DIFFRACTION100
4.225-4.48960.22561410.18513192X-RAY DIFFRACTION100
4.4896-4.8360.22141410.17853210X-RAY DIFFRACTION100
4.836-5.32210.24841440.18773234X-RAY DIFFRACTION100
5.3221-6.09120.22051440.21063248X-RAY DIFFRACTION100
6.0912-7.66990.22941460.19863290X-RAY DIFFRACTION100
7.6699-50.65450.1641540.15073489X-RAY DIFFRACTION100

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