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- PDB-2z5o: Complex of Transportin 1 with JKTBP NLS -

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Basic information

Entry
Database: PDB / ID: 2z5o
TitleComplex of Transportin 1 with JKTBP NLS
Components
  • Heterogeneous nuclear ribonucleoprotein D-like
  • Transportin-1
KeywordsTRANSPORT PROTEIN/RNA BINDING PROTEIN / nuclear transport / importin / exportin / karyopherin / nucleocytoplasmic / hnRNP / NLS / NES / TRANSPORT PROTEIN-RNA BINDING PROTEIN COMPLEX
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 / small GTPase binding / cilium / 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 / small GTPase binding / cilium / protein import into nucleus / RNA binding / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT repeat / HEAT repeat / HEAT-like 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 repeat / HEAT repeat / HEAT-like 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: 3.2 Å
AuthorsImasaki, T. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Kose, S. / Imamoto, N. / 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 14, 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
Remark 999SEQUENCE Because the electron density for all amino acids of protein in chain B was poor, the ...SEQUENCE Because the electron density for all amino acids of protein in chain B was poor, the authors were unable to assign side chains of them. In addition, residue numbers are arbitrary, not consistent with the UNP residues numbering. The following is the one-letter sequence for the protein in chain B modeled in this structure, UniProtKB entry O14979(residues 396-420): YSGQQSTYGKASRGGGNHQNNYQPY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transportin-1
B: Heterogeneous nuclear ribonucleoprotein D-like


Theoretical massNumber of molelcules
Total (without water)102,2782
Polymers102,2782
Non-polymers00
Water00
1
A: Transportin-1


Theoretical massNumber of molelcules
Total (without water)101,4081
Polymers101,4081
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heterogeneous nuclear ribonucleoprotein D-like


  • defined by author
  • 869 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8691
Polymers8691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.306, 169.805, 68.458
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 Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 101408.438 Da / Num. of mol.: 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
#2: Protein/peptide Heterogeneous nuclear ribonucleoprotein D-like


Mass: 869.063 Da / Num. of mol.: 1 / Fragment: Region of interest in the sequence / Source method: obtained synthetically
Details: Chemical synthesis. This sequence occurs naturally in humans.

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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: 3.76 Å3/Da / Density % sol: 67.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1M Tris-HCl pH 8.6, 14% (w/v) PEG 8000, 0.1M NaH2PO4, 0.015mM Phenol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jul 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 25190 / Num. obs: 23669 / % possible obs: 94.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.2
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.6 / % possible all: 82.8

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Processing

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

1qbk


Resolution: 3.2→47.57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 54.103 / SU ML: 0.408 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27859 1265 5.1 %RANDOM
Rwork0.23551 ---
obs0.23765 23669 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 129.703 Å2
Baniso -1Baniso -2Baniso -3
1--10.35 Å20 Å20 Å2
2--15.29 Å20 Å2
3----4.94 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6689 0 0 0 6689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226829
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9779276
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5695841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.25325.197304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.72151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741531
X-RAY DIFFRACTIONr_chiral_restr0.080.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025099
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.23660
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24800
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.281.54363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.51226874
X-RAY DIFFRACTIONr_scbond_it0.49632774
X-RAY DIFFRACTIONr_scangle_it0.8584.52402
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 71 -
Rwork0.35 1494 -
obs--82.02 %
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)
13.65181.73190.52232.45130.66431.89450.0229-0.29870.2154-0.0475-0.1623-0.4108-0.05240.00570.1394-0.33780.02090.0244-0.1233-0.0329-0.319635.0489-15.114-12.5679
24.6897-0.8873-1.48732.30960.89794.40.03340.632-0.205-0.0755-0.1209-0.14760.12620.17980.0875-0.3497-0.034-0.0952-0.3638-0.094-0.48525.1439-38.1928-47.7217
32.6332.86220.43637.46671.2361.23690.3628-0.1536-0.16020.7506-0.0829-0.16820.4209-0.0515-0.2799-0.17090.1473-0.1063-0.2127-0.0497-0.009346.7037-70.3069-38.4592
460.1992-47.0498-9.837937.10744.475132.4636-3.3036-2.2523-3.4771.12763.8199-3.05232.16043.8402-0.5163-0.005-0.0145-0.0063-0.0022-0.01720.000428.0642-33.8235-35.5124
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 3196 - 319
2X-RAY DIFFRACTION2AA371 - 603371 - 603
3X-RAY DIFFRACTION3AA604 - 890604 - 890
4X-RAY DIFFRACTION4BB1 - 101 - 10

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