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- PDB-2z5n: Complex of Transportin 1 with hnRNP D NLS -

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Basic information

Entry
Database: PDB / ID: 2z5n
TitleComplex of Transportin 1 with hnRNP D NLS
Components
  • Heterogeneous nuclear ribonucleoprotein D0
  • 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


hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / : / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / response to sodium phosphate ...hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / : / mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / response to sodium phosphate / Intraflagellar transport / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / RNA catabolic process / Postmitotic nuclear pore complex (NPC) reformation / regulation of telomere maintenance / nuclear import signal receptor activity / nuclear localization sequence binding / telomeric DNA binding / minor groove of adenine-thymine-rich DNA binding / positive regulation of telomere capping / Processing of Capped Intron-Containing Pre-mRNA / cellular response to nitric oxide / RNA processing / response to electrical stimulus / mRNA Splicing - Major Pathway / cerebellum development / liver development / AUF1 (hnRNP D0) binds and destabilizes mRNA / cellular response to estradiol stimulus / positive regulation of translation / cellular response to amino acid stimulus / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / small GTPase binding / cilium / histone deacetylase binding / response to calcium ion / protein import into nucleus / regulation of gene expression / postsynaptic density / ribonucleoprotein complex / negative regulation of gene expression / glutamatergic synapse / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
CARG-binding factor, N-terminal / CBFNT (NUC161) domain / 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 ...CARG-binding factor, N-terminal / CBFNT (NUC161) domain / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein D0 / Transportin-1
Similarity search - Component
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transportin-1
B: Heterogeneous nuclear ribonucleoprotein D0


Theoretical massNumber of molelcules
Total (without water)104,1752
Polymers104,1752
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 D0


Theoretical massNumber of molelcules
Total (without water)2,7671
Polymers2,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.683, 118.954, 151.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 D0 / hnRNP D0 / AU-rich element RNA-binding protein 1 / hnRNP D NLS


Mass: 2766.960 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 332-355 / Source method: obtained synthetically
Details: Chemical synthesis. This sequence occurs naturally in humans.
References: UniProt: Q14103

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1M Tris-HCl pH 8.8, 16-20%(w/v) PEG 8000, 0.1M KCl, 0.1M NaH2PO4, 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: Apr 9, 2006
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: 19679 / Num. obs: 18626 / % possible obs: 91.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.2
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 1.7 / % possible all: 56.4

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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 2Z5O

2z5o


Resolution: 3.2→45.22 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 67.841 / SU ML: 0.478 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.599 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29525 1017 5.2 %RANDOM
Rwork0.23187 ---
obs0.23493 18626 91.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.718 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å20 Å20 Å2
2---3.05 Å20 Å2
3---6.35 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6817 0 0 0 6817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9769455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0625852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.725.111315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.164151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5721533
X-RAY DIFFRACTIONr_chiral_restr0.0740.21081
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025209
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.23962
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24917
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2661.54389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48726972
X-RAY DIFFRACTIONr_scbond_it0.51832871
X-RAY DIFFRACTIONr_scangle_it0.9214.52483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.199→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 22 -
Rwork0.346 765 -
obs--51.64 %
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)
16.9917-0.912-2.02410.1230.17462.5512-0.4536-0.5281-0.0760.51870.1188-0.8606-1.60520.07170.33480.6672-0.2635-0.12040.0741-0.09280.359634.145520.468263.6151
25.24160.5236-1.30782.04261.156.90230.4481-0.09270.6540.5255-0.5227-0.1632-1.99660.92510.0746-0.0378-0.3321-0.1125-0.14220.10070.349741.574913.532852.8064
35.71171.31442.42631.8353-0.2472.3740.18040.1536-0.2611-0.1945-0.3049-0.49070.03530.56860.1245-0.49180.18750.232-0.22350.38650.034438.2736-7.499832.2695
43.6304-1.38370.9345.88-2.09612.96440.0753-0.3905-0.6324-0.30040.06280.35760.3231-0.2506-0.1381-0.7233-0.00060.0591-0.57990.0858-0.66810.4543-1.498721.5405
51.9763-0.6002-0.91971.40961.85796.3126-0.18960.1513-0.2833-0.15320.2734-0.3852-0.25810.5793-0.0838-0.3664-0.13640.1417-0.5653-0.0235-0.428512.263517.3043-4.1276
63.11091.69711.46556.9711-7.57112.2804-0.08740.29780.6497-0.1569-0.1951-0.662-0.8626-0.06740.2825-0.25450.25090.3699-0.36370.1518-0.25839.05375.45917.5488
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 DIFFRACTION4AA366 - 603366 - 603
5X-RAY DIFFRACTION5AA604 - 890604 - 890
6X-RAY DIFFRACTION6BB341 - 35510 - 24

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