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- PDB-2z5m: Complex of Transportin 1 with TAP NLS, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 2z5m
TitleComplex of Transportin 1 with TAP NLS, crystal form 2
Components
  • Nuclear RNA export factor 1
  • Transportin-1
KeywordsTRANSPORT PROTEIN/RNA BINDING PROTEIN / nuclear transport / importin / exportin / karyopherin / nucleocytoplasmic / TAP / NLS / TRANSPORT PROTEIN-RNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


nuclear RNA export factor complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity ...nuclear RNA export factor complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / small GTPase binding / protein import into nucleus / cytoplasmic stress granule / protein transport / cilium / nuclear speck / mRNA binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote ...Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Importin beta family / HEAT-like repeat / Nuclear transport factor 2 domain / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / UBA-like superfamily / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / NTF2-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / RNA-binding domain superfamily / Leucine-rich repeat domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Transportin-1 / Nuclear RNA export factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Transportin-1
B: Nuclear RNA export factor 1


Theoretical massNumber of molelcules
Total (without water)104,8952
Polymers104,8952
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: Nuclear RNA export factor 1


Theoretical massNumber of molelcules
Total (without water)3,4871
Polymers3,4871
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.442, 170.986, 68.340
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 Nuclear RNA export factor 1 / Tip-associating protein / Tip-associated protein / mRNA export factor TAP / TAP NLS


Mass: 3486.679 Da / Num. of mol.: 1 / Fragment: Nuclear export signal, UNP residues 53-82 / Source method: obtained synthetically
Details: Chemical synthesis. This sequence occurs naturally in humans.
References: UniProt: Q9UBU9

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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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 100mM Tris-HCl pH 8.8, 16-18% (w/v) PEG 8000, 0.1M NaH2PO4, 0.1M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 31175 / Num. obs: 28901 / % possible obs: 95.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.8 / % possible all: 71.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z5O

2z5o


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.046 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.499 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26741 1532 5 %RANDOM
Rwork0.24797 ---
obs0.24899 28901 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.159 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å20 Å20 Å2
2--6.24 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 0 0 6778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226925
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9779408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4495847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34225.112313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.279151238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.361533
X-RAY DIFFRACTIONr_chiral_restr0.0770.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025175
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.23627
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24917
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.54380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93826939
X-RAY DIFFRACTIONr_scbond_it1.2132833
X-RAY DIFFRACTIONr_scangle_it1.6614.52469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 72 -
Rwork0.335 1555 -
obs--70.43 %

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