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- PDB-7vpw: Crystal structure of Transportin-1 in complex with BAP1 PY-NLS (r... -

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Basic information

Entry
Database: PDB / ID: 7vpw
TitleCrystal structure of Transportin-1 in complex with BAP1 PY-NLS (residues 706-724)
Components
  • BRCA1-associated protein 1 (BAP1)
  • Transportin-1
KeywordsPROTEIN TRANSPORT / Transportin-1 / BRCA1-associated protein 1 / BAP1 / nuclear import / PY-NLS / deubiquitinase / DUB
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / nuclear localization sequence binding / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / protein deubiquitination / small GTPase binding / protein import into nucleus / ubiquitin-dependent protein catabolic process / cysteine-type deubiquitinase activity ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / nuclear localization sequence binding / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / protein deubiquitination / small GTPase binding / protein import into nucleus / ubiquitin-dependent protein catabolic process / cysteine-type deubiquitinase activity / cilium / nucleolus / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Importin beta family / HEAT-like repeat / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. ...Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Importin beta family / HEAT-like repeat / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase BAP1 / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.76 Å
AuthorsYang, T.J. / Hsu, S.T.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-001-050-MY3 Taiwan
CitationJournal: J.Cell Biol. / Year: 2022
Title: Tumor suppressor BAP1 nuclear import is governed by transportin-1.
Authors: Yang, T.J. / Li, T.N. / Huang, R.S. / Pan, M.Y. / Lin, S.Y. / Lin, S. / Wu, K.P. / Wang, L.H. / Hsu, S.D.
History
DepositionOct 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: BRCA1-associated protein 1 (BAP1)
A: Transportin-1


Theoretical massNumber of molelcules
Total (without water)100,9702
Polymers100,9702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.896, 129.688, 170.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein/peptide BRCA1-associated protein 1 (BAP1)


Mass: 2457.929 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: B3KS40
#2: Protein Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 98511.586 Da / Num. of mol.: 1
Fragment: UNP residues 8-344, UNP residues 376-898,UNP residues 376-898
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, TNPO1, KPNB2, MIP1, TRN / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / 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: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.49 M Sodium phosphate monobasic monohydrate, 0.91 M Sodium phosphate dibasic, pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.76→103.2 Å / Num. obs: 16059 / % possible obs: 99.6 % / Redundancy: 6.88 % / Biso Wilson estimate: 133.33 Å2 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.09 / Rsym value: 0.23 / Net I/σ(I): 7.3
Reflection shellResolution: 3.76→3.88 Å / Num. unique obs: 795 / CC1/2: 0.905

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2z5o

2z5o


Resolution: 3.76→63.86 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1588 10.02 %
Rwork0.2293 14261 -
obs0.2324 15849 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.16 Å2 / Biso mean: 145.5931 Å2 / Biso min: 81.11 Å2
Refinement stepCycle: final / Resolution: 3.76→63.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6705 0 0 0 6705
Num. residues----841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.76-3.880.37631340.33531200133493
3.88-4.020.38381400.30381250139096
4.02-4.180.31371430.27381286142999
4.18-4.370.33011420.28091281142399
4.37-4.60.33211450.2541296144199
4.61-4.890.28311440.250212971441100
4.89-5.270.27161450.251213001445100
5.27-5.80.28881470.273613121459100
5.8-6.640.28591460.245413181464100
6.64-8.360.22681500.204413431493100
8.36-63.860.18631520.16971378153096

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