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- PDB-4c0p: Unliganded Transportin 3 -

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Basic information

Entry
Database: PDB / ID: 4c0p
TitleUnliganded Transportin 3
ComponentsTRANSPORTIN-3
KeywordsTRANSPORT PROTEIN / NUCLEAR IMPORT / HEAT REPEAT / TNPO3
Function / homology
Function and homology information


annulate lamellae / nuclear import signal receptor activity / small GTPase binding / protein import into nucleus / nuclear envelope / nucleoplasm / identical protein binding / 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 / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Transportin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMaertens, G.N. / Cook, N.J. / Hare, S. / 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 / 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 / _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: TRANSPORTIN-3
B: TRANSPORTIN-3
C: TRANSPORTIN-3
D: TRANSPORTIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,7428
Polymers417,1254
Non-polymers6174
Water00
1
A: TRANSPORTIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4352
Polymers104,2811
Non-polymers1541
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRANSPORTIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4352
Polymers104,2811
Non-polymers1541
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRANSPORTIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4352
Polymers104,2811
Non-polymers1541
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TRANSPORTIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4352
Polymers104,2811
Non-polymers1541
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.198, 104.019, 124.890
Angle α, β, γ (deg.)90.64, 97.88, 104.48
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96263, 0.01746, -0.27025), (0.00426, -0.99682, -0.07957), (-0.27078, -0.07775, 0.9595)-31.16096, -18.83201, 57.43454
2given(-0.8722, -0.48913, 0.00404), (-0.4891, 0.8722, 0.00713), (-0.00701, 0.00424, -0.99997)-47.69779, 40.47414, 63.21891
3given(0.84657, 0.46581, 0.25755), (0.4645, -0.88281, 0.06984), (0.2599, 0.0605, -0.96374)14.68144, -60.13893, 4.54737

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Components

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


Mass: 104281.148 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C511A MUTATION ENGINEERED TO IMPROVE CRYSTAL PACKING
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: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
Sequence detailsC511A MUTATION ENGINEERED TO IMPROVE CRYSTAL PACKING

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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: 2.88 Å3/Da / Density % sol: 57.3 % / Description: NONE
Crystal growpH: 8.2
Details: 20% (W/V) PEG3350, 0.2 M NABR, 10 MM DTT, 2 MM EDTA, 0.1 M BIS-TRIS PROPANE, PH8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 96311 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 78.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.1
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.4 / % possible all: 98.7

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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 2X19, 2XWU

2x19

2xwu


Resolution: 2.95→38.17 Å / SU ML: 0.44 / σ(F): 1.96 / Phase error: 30.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 4834 5 %
Rwork0.2358 --
obs0.2373 95818 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.8 Å2
Refinement stepCycle: LAST / Resolution: 2.95→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28261 0 32 0 28293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328849
X-RAY DIFFRACTIONf_angle_d0.77139159
X-RAY DIFFRACTIONf_dihedral_angle_d15.12310637
X-RAY DIFFRACTIONf_chiral_restr0.0294601
X-RAY DIFFRACTIONf_plane_restr0.0044985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.98350.44271590.41673110X-RAY DIFFRACTION98
2.9835-3.01860.40451420.35482969X-RAY DIFFRACTION98
3.0186-3.05540.36951810.33113072X-RAY DIFFRACTION98
3.0554-3.09410.31671680.29452993X-RAY DIFFRACTION98
3.0941-3.13470.31591590.29223039X-RAY DIFFRACTION98
3.1347-3.17770.31761570.28633022X-RAY DIFFRACTION99
3.1777-3.2230.34151610.29913068X-RAY DIFFRACTION99
3.223-3.27110.33351450.26793075X-RAY DIFFRACTION99
3.2711-3.32220.30261480.2663055X-RAY DIFFRACTION98
3.3222-3.37660.32691590.27993054X-RAY DIFFRACTION99
3.3766-3.43480.3151550.2713075X-RAY DIFFRACTION99
3.4348-3.49730.33421650.25963039X-RAY DIFFRACTION99
3.4973-3.56450.26731580.25423058X-RAY DIFFRACTION99
3.5645-3.63720.29211680.25983009X-RAY DIFFRACTION98
3.6372-3.71620.31241790.25983076X-RAY DIFFRACTION99
3.7162-3.80260.33321530.25142991X-RAY DIFFRACTION98
3.8026-3.89760.30251630.25383047X-RAY DIFFRACTION98
3.8976-4.00280.28871830.22793022X-RAY DIFFRACTION98
4.0028-4.12050.25571590.22543010X-RAY DIFFRACTION98
4.1205-4.25330.25581730.22622982X-RAY DIFFRACTION98
4.2533-4.40510.27981510.22853063X-RAY DIFFRACTION98
4.4051-4.58120.26211790.22283037X-RAY DIFFRACTION98
4.5812-4.78940.26831540.2213054X-RAY DIFFRACTION99
4.7894-5.04130.26071720.20462998X-RAY DIFFRACTION98
5.0413-5.35640.23131630.21463058X-RAY DIFFRACTION99
5.3564-5.76870.27161350.22883069X-RAY DIFFRACTION99
5.7687-6.34680.23821720.22583050X-RAY DIFFRACTION99
6.3468-7.25970.23411540.20923055X-RAY DIFFRACTION99
7.2597-9.12580.16151660.18753017X-RAY DIFFRACTION98
9.1258-38.1730.22031530.21252817X-RAY DIFFRACTION91

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