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- PDB-2z5j: Free Transportin 1 -

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Basic information

Entry
Database: PDB / ID: 2z5j
TitleFree Transportin 1
ComponentsTransportin-1
KeywordsTRANSPORT PROTEIN / nuclear transport / importin / exportin / karyopherin / nucleocytoplasmic
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / cilium / small GTPase binding / protein import into nucleus / RNA binding / extracellular exosome ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / cilium / small GTPase binding / protein import into nucleus / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin beta family / HEAT-like repeat / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...Importin beta family / HEAT-like repeat / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsImasaki, T. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Yamada, M. / Sato, M.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis for substrate recognition and dissociation by human transportin 1
Authors: Imasaki, T. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Kose, S. / Imamoto, N. / Yamada, M. / Sato, M.
History
DepositionJul 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transportin-1


Theoretical massNumber of molelcules
Total (without water)101,4081
Polymers101,4081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.467, 107.467, 194.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 101408.438 Da / Num. of mol.: 1 / Fragment: Transportin 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92973

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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: 55.64 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9.8
Details: 6% PEG 8000, 0.1M sodium dihidrogen phosphate, 0.1M CAPSO pH 9.8, 0.04M spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→94 Å / Num. all: 15598 / Num. obs: 14806 / % possible obs: 94.8 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.7 / % possible all: 72.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBK

1qbk


Resolution: 3.4→49.36 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.871 / SU B: 94.867 / SU ML: 0.648 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.714 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30301 778 5 %RANDOM
Rwork0.23226 ---
obs0.2358 14806 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.231 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--1.29 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 0 0 6652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9779232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.29125.18305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.613151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0011531
X-RAY DIFFRACTIONr_chiral_restr0.0740.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025073
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.23936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24794
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.040.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2441.54272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.44626813
X-RAY DIFFRACTIONr_scbond_it0.45732798
X-RAY DIFFRACTIONr_scangle_it0.7984.52419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.398→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 33 -
Rwork0.439 785 -
obs--69.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.9262-3.396-2.67590.89240.74548.38510.4709-0.89221.51930.61610.19560.2022-1.5407-0.164-0.66650.0949-0.06050.2848-0.2647-0.30380.1193-30.469460.96586.5742
210.8061-1.69140.68287.5445-0.23639.32620.5448-0.16230.7031-0.1625-0.29970.25920.0686-0.1463-0.2451-0.49750.13530.1284-0.6536-0.0926-0.5712-28.81953.1632-5.9957
32.78380.0171-1.98876.5334-2.44573.2951-0.41820.0042-0.716-0.37310.2619-0.02540.7536-0.03730.1563-0.3149-0.07120.0389-0.4287-0.0494-0.4842-22.906926.3949-16.103
45.45130.0809-1.84221.64790.18052.21590.0766-0.8482-0.80470.1563-0.0883-0.44380.07720.17270.0117-0.2258-0.0878-0.1919-0.38630.3744-0.1627-42.70345.832511.5875
52.50511.52820.60687.37362.36812.7147-0.0725-0.0507-0.2948-0.0082-0.0086-0.0840.34960.03250.0812-0.68970.0340.0864-0.47260.1789-0.6786-73.1475-0.3185-7.6027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 575 - 57
2X-RAY DIFFRACTION2AA58 - 12558 - 125
3X-RAY DIFFRACTION3AA126 - 319126 - 319
4X-RAY DIFFRACTION4AA371 - 603371 - 603
5X-RAY DIFFRACTION5AA604 - 890604 - 890

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