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- PDB-7cyl: Crystal structure of Karyopherin-beta2 in complex with FUS PY-NLS... -

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Basic information

Entry
Database: PDB / ID: 7cyl
TitleCrystal structure of Karyopherin-beta2 in complex with FUS PY-NLS(P525L)
Components
  • RNA-binding protein FUS
  • Transportin-1
KeywordsTRANSPORT PROTEIN/RNA BINDING PROTEIN / Nuclear import / Karyopherin / TRANSPORT PROTEIN / TRANSPORT PROTEIN-RNA BINDING PROTEIN complex
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / mRNA stabilization / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / intracellular non-membrane-bounded organelle / nuclear localization sequence binding / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / mRNA stabilization / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / intracellular non-membrane-bounded organelle / nuclear localization sequence binding / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / mRNA Splicing - Major Pathway / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / transcription coregulator activity / protein homooligomerization / small GTPase binding / cilium / protein import into nucleus / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
TAF15/EWS/TLS family / 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 / Zinc finger domain ...TAF15/EWS/TLS family / 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 / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA-binding protein FUS / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYoshizawa, T. / Chook, Y.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM069909 United States
CitationJournal: Sci Rep / Year: 2021
Title: Mechanism of karyopherin-beta 2 binding and nuclear import of ALS variants FUS(P525L) and FUS(R495X).
Authors: Gonzalez, A. / Mannen, T. / Cagatay, T. / Fujiwara, A. / Matsumura, H. / Niesman, A.B. / Brautigam, C.A. / Chook, Y.M. / Yoshizawa, T.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: RNA-binding protein FUS


Theoretical massNumber of molelcules
Total (without water)104,1142
Polymers104,1142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-5 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.190, 158.366, 68.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 98325.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, KPNB2, MIP1, TRN / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q92973
#2: Protein RNA-binding protein FUS / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 5788.235 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUS, TLS / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P35637

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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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1 M Succinic acid (pH7.0), 1%(w/v) PEG MME2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.7→47.06 Å / Num. obs: 39428 / % possible obs: 99.69 % / Redundancy: 7 % / Biso Wilson estimate: 75.89 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.3
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3860 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDD

4fdd


Resolution: 2.7→47.06 Å / SU ML: 0.311 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.0032
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 1972 5 %
Rwork0.1963 37455 -
obs0.198 39427 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6827 0 0 0 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046972
X-RAY DIFFRACTIONf_angle_d1.45689462
X-RAY DIFFRACTIONf_chiral_restr0.09441078
X-RAY DIFFRACTIONf_plane_restr0.00991221
X-RAY DIFFRACTIONf_dihedral_angle_d20.70462632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.32851370.30082613X-RAY DIFFRACTION98.74
2.77-2.840.32761380.28622632X-RAY DIFFRACTION99.93
2.84-2.930.2911400.25982648X-RAY DIFFRACTION99.86
2.93-3.020.3391370.25712612X-RAY DIFFRACTION99.93
3.02-3.130.27261410.24212673X-RAY DIFFRACTION99.86
3.13-3.250.26741400.23342640X-RAY DIFFRACTION99.68
3.25-3.40.26211390.22982645X-RAY DIFFRACTION99.93
3.4-3.580.2811400.22552668X-RAY DIFFRACTION100
3.58-3.80.24761410.20682670X-RAY DIFFRACTION100
3.81-4.10.23321410.18752682X-RAY DIFFRACTION99.93
4.1-4.510.22361410.16972676X-RAY DIFFRACTION99.93
4.51-5.160.19081420.17472710X-RAY DIFFRACTION99.96
5.16-6.50.24411450.21162744X-RAY DIFFRACTION99.97
6.5-47.060.16991500.15652842X-RAY DIFFRACTION98.55
Refinement TLS params.Method: refined / Origin x: 29.534630176 Å / Origin y: 40.7075505528 Å / Origin z: 30.7826833689 Å
111213212223313233
T0.531012596858 Å20.0350728124082 Å2-0.00679642924534 Å2-0.488887516363 Å2-0.0536421787596 Å2--0.405193575401 Å2
L1.17460007189 °2-0.268717522089 °20.422280770994 °2-0.760109088605 °2-0.381124378559 °2--0.349416598187 °2
S0.182831697563 Å °-0.0654599696842 Å °-0.15175322095 Å °-0.0686380443344 Å °-0.104401070647 Å °0.11581761067 Å °0.0644805496489 Å °-0.0312707256654 Å °0.042556881633 Å °
Refinement TLS groupSelection details: all

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