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- PDB-4c0o: Transportin 3 in complex with phosphorylated ASF/SF2 -

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Basic information

Entry
Database: PDB / ID: 4c0o
TitleTransportin 3 in complex with phosphorylated ASF/SF2
Components
  • SERINE/ARGININE-RICH SPLICING FACTOR 1
  • TRANSPORTIN-3
KeywordsTRANSPORT PROTEIN/RNA BINDING PROTEIN / TRANSPORT PROTEIN-RNA BINDING PROTEIN COMPLEX / NUCLEAR IMPORT / HEAT REPEAT / SPLICING FACTOR / RRM DOMAIN / RS DOMAIN
Function / homology
Function and homology information


DNA topoisomerase binding / protein kinase B binding / annulate lamellae / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear import signal receptor activity / regulation of RNA splicing ...DNA topoisomerase binding / protein kinase B binding / annulate lamellae / alternative mRNA splicing, via spliceosome / mRNA splice site recognition / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / nuclear import signal receptor activity / regulation of RNA splicing / oligodendrocyte differentiation / mRNA 5'-splice site recognition / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / liver regeneration / mRNA splicing, via spliceosome / small GTPase binding / mRNA processing / protein import into nucleus / nuclear envelope / nuclear speck / mRNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transportin-3/Importin-13 second TPR domain / Transportin-3/Importin-13 third TPR domain / Transportin-3/Importin-13 fourth TPR domain / : / SRSF1, RNA recognition motif 1 / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / : / RRM (RNA recognition motif) domain ...Transportin-3/Importin-13 second TPR domain / Transportin-3/Importin-13 third TPR domain / Transportin-3/Importin-13 fourth TPR domain / : / SRSF1, RNA recognition motif 1 / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / : / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Serine/arginine-rich splicing factor 1 / Transportin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.557 Å
AuthorsMaertens, G.N. / Cook, N.J. / Cherepanov, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural Basis for Nuclear Import of Splicing Factors by Human Transportin 3.
Authors: Maertens, G.N. / Cook, N.J. / Wang, W. / Hare, S. / Gupta, S.S. / Oztop, I. / Lee, K. / Pye, V.E. / Cosnefroy, O. / Snijders, A.P. / Kewalramani, V.N. / Fassati, A. / Engelman, A. / Cherepanov, P.
History
DepositionAug 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references / Structure summary
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Mar 5, 2014Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: SERINE/ARGININE-RICH SPLICING FACTOR 1
D: SERINE/ARGININE-RICH SPLICING FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,7775
Polymers237,7384
Non-polymers391
Water91951
1
A: TRANSPORTIN-3
C: SERINE/ARGININE-RICH SPLICING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)118,8692
Polymers118,8692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-0.6 kcal/mol
Surface area43680 Å2
MethodPISA
2
B: TRANSPORTIN-3
D: SERINE/ARGININE-RICH SPLICING FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9083
Polymers118,8692
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint1.4 kcal/mol
Surface area43530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.552, 91.062, 98.122
Angle α, β, γ (deg.)106.98, 100.30, 102.18
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.47944, -0.87486, 0.06904), (-0.87581, -0.48197, -0.02552), (0.0556, -0.04823, -0.99729)-3.29811, -0.03558, 73.78626
2given(0.4915, -0.8674, 0.0777), (-0.86754, -0.49547, -0.04345), (0.07619, -0.04605, -0.99603)-3.10669, -0.54983, 73.42142

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Components

#1: Protein TRANSPORTIN-3 / IMPORTIN-12 / IMP12 / TRANSPORTIN-SR / TRN-SR / TRANSPORTIN 3


Mass: 104313.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETSUMO-TNPO3(C511A) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 LAC I / References: UniProt: Q9Y5L0
#2: Protein SERINE/ARGININE-RICH SPLICING FACTOR 1 / ALTERNATIVE-SPLICING FACTOR 1 / ASF-1 / SPLICING FACTOR / ARGI NINE/SERINE-RICH 1 / PRE-MRNA- ...ALTERNATIVE-SPLICING FACTOR 1 / ASF-1 / SPLICING FACTOR / ARGI NINE/SERINE-RICH 1 / PRE-MRNA-SPLICING FACTOR SF2 / P33 SUBUNIT / SFR S1


Mass: 14555.848 Da / Num. of mol.: 2
Fragment: RESIDUES 106-230 (SECOND RRM DOMAIN AND RS DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETSUMO-SFRS1(106-230) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: Q07955
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFRAGMENT 106-230

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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: 2.77 Å3/Da / Density % sol: 55.7 % / Description: NONE
Crystal growpH: 6
Details: 16% (W/V) PEG3350, 0.1 M KSCN, 0.1 M BIS-TRIS PROPANE, PH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.57→47.3 Å / Num. obs: 80114 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 73.42 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3BEG AND 4C0P

3beg

4c0p


Resolution: 2.557→38.283 Å / SU ML: 0.44 / σ(F): 1.96 / Phase error: 32.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2691 4037 5.1 %
Rwork0.2212 --
obs0.2236 79944 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.51 Å2
Refinement stepCycle: LAST / Resolution: 2.557→38.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15806 0 1 51 15858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516117
X-RAY DIFFRACTIONf_angle_d0.92421874
X-RAY DIFFRACTIONf_dihedral_angle_d16.45970
X-RAY DIFFRACTIONf_chiral_restr0.0362531
X-RAY DIFFRACTIONf_plane_restr0.0052799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5575-2.58760.42331110.32961908X-RAY DIFFRACTION71
2.5876-2.61910.39241340.33772619X-RAY DIFFRACTION98
2.6191-2.65230.39711300.31062613X-RAY DIFFRACTION98
2.6523-2.68720.35271470.30342660X-RAY DIFFRACTION98
2.6872-2.7240.36341390.31192603X-RAY DIFFRACTION99
2.724-2.76290.38771470.30522637X-RAY DIFFRACTION99
2.7629-2.80410.3621320.31292636X-RAY DIFFRACTION99
2.8041-2.84790.38891530.31182629X-RAY DIFFRACTION99
2.8479-2.89460.38561410.30192631X-RAY DIFFRACTION99
2.8946-2.94450.39991460.29022658X-RAY DIFFRACTION100
2.9445-2.9980.31881540.27452635X-RAY DIFFRACTION99
2.998-3.05560.33091300.25972658X-RAY DIFFRACTION99
3.0556-3.1180.29311240.26422683X-RAY DIFFRACTION100
3.118-3.18570.30511200.26582665X-RAY DIFFRACTION100
3.1857-3.25980.30041380.27232667X-RAY DIFFRACTION100
3.2598-3.34130.34511400.27172637X-RAY DIFFRACTION99
3.3413-3.43160.31651480.26512612X-RAY DIFFRACTION100
3.4316-3.53250.28211580.25072679X-RAY DIFFRACTION99
3.5325-3.64640.31351430.24642658X-RAY DIFFRACTION100
3.6464-3.77660.29481510.23992629X-RAY DIFFRACTION99
3.7766-3.92770.29061280.22832655X-RAY DIFFRACTION99
3.9277-4.10620.23731230.21612670X-RAY DIFFRACTION99
4.1062-4.32240.25841460.21042647X-RAY DIFFRACTION99
4.3224-4.59280.22381300.20472636X-RAY DIFFRACTION99
4.5928-4.94680.23181390.19672665X-RAY DIFFRACTION99
4.9468-5.44330.25461380.20572646X-RAY DIFFRACTION99
5.4433-6.22810.27391610.21882611X-RAY DIFFRACTION99
6.2281-7.83570.24341540.19382635X-RAY DIFFRACTION99
7.8357-38.2870.17381320.14132625X-RAY DIFFRACTION98

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