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- PDB-5yvg: Crystal structure of Karyopherin beta2 in complex with FUS(full l... -

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Basic information

Entry
Database: PDB / ID: 5yvg
TitleCrystal structure of Karyopherin beta2 in complex with FUS(full length)
Components
  • RNA-binding protein FUS
  • Transportin-1
KeywordsPROTEIN TRANSPORT/RNA BINDING PROTEIN / Importin family / PROTEIN TRANSPORT / PROTEIN TRANSPORT-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: 4.05 Å
AuthorsYoshizawa, T. / Fung, H.Y.J. / Chook, Y.M.
CitationJournal: Cell / Year: 2018
Title: Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites.
Authors: Yoshizawa, T. / Ali, R. / Jiou, J. / Fung, H.Y.J. / Burke, K.A. / Kim, S.J. / Lin, Y. / Peeples, W.B. / Saltzberg, D. / Soniat, M. / Baumhardt, J.M. / Oldenbourg, R. / Sali, A. / Fawzi, N.L. ...Authors: Yoshizawa, T. / Ali, R. / Jiou, J. / Fung, H.Y.J. / Burke, K.A. / Kim, S.J. / Lin, Y. / Peeples, W.B. / Saltzberg, D. / Soniat, M. / Baumhardt, J.M. / Oldenbourg, R. / Sali, A. / Fawzi, N.L. / Rosen, M.K. / Chook, Y.M.
History
DepositionNov 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transportin-1
B: Transportin-1
X: RNA-binding protein FUS
Y: RNA-binding protein FUS


Theoretical massNumber of molelcules
Total (without water)303,8984
Polymers303,8984
Non-polymers00
Water00
1
A: Transportin-1
X: RNA-binding protein FUS


Theoretical massNumber of molelcules
Total (without water)151,9492
Polymers151,9492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transportin-1
Y: RNA-binding protein FUS


Theoretical massNumber of molelcules
Total (without water)151,9492
Polymers151,9492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.219, 145.015, 108.681
Angle α, β, γ (deg.)90.000, 94.552, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASNASN(chain 'A' and (resid 11 through 41 or resid 50...AA11 - 4113 - 43
12LEULEUPHEPHE(chain 'A' and (resid 11 through 41 or resid 50...AA50 - 8052 - 82
13GLYGLYILEILE(chain 'A' and (resid 11 through 41 or resid 50...AA86 - 11788 - 119
14TRPTRPASPASP(chain 'A' and (resid 11 through 41 or resid 50...AA126 - 138128 - 140
15CYSCYSLEULEU(chain 'A' and (resid 11 through 41 or resid 50...AA145 - 163147 - 165
16ASNASNPHEPHE(chain 'A' and (resid 11 through 41 or resid 50...AA173 - 183175 - 185
17PROPROILEILE(chain 'A' and (resid 11 through 41 or resid 50...AA188 - 202190 - 204
18LEULEUVALVAL(chain 'A' and (resid 11 through 41 or resid 50...AA211 - 245213 - 247
19HISHISLEULEU(chain 'A' and (resid 11 through 41 or resid 50...AA253 - 317255 - 319
110SERSERVALVAL(chain 'A' and (resid 11 through 41 or resid 50...AA371 - 389349 - 367
111LEULEUILEILE(chain 'A' and (resid 11 through 41 or resid 50...AA395 - 424373 - 402
112METMETVALVAL(chain 'A' and (resid 11 through 41 or resid 50...AA429 - 552407 - 530
113LEULEUGLNGLN(chain 'A' and (resid 11 through 41 or resid 50...AA556 - 863534 - 841
114ASPASPTYRTYR(chain 'A' and (resid 11 through 41 or resid 50...AA866 - 888844 - 866
215GLYGLYASNASN(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB11 - 4113 - 43
216LEULEUPHEPHE(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB50 - 8052 - 82
217GLYGLYILEILE(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB86 - 11788 - 119
218TRPTRPASPASP(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB126 - 138128 - 140
219CYSCYSLEULEU(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB145 - 163147 - 165
220ASNASNPHEPHE(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB173 - 183175 - 185
221PROPROILEILE(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB188 - 202190 - 204
222LEULEUVALVAL(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB211 - 245213 - 247
223HISHISLEULEU(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB253 - 317255 - 319
224SERSERVALVAL(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB371 - 389349 - 367
225LEULEUILEILE(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB395 - 424373 - 402
226METMETVALVAL(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB429 - 552407 - 530
227LEULEUGLNGLN(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB556 - 863534 - 841
228ASPASPTYRTYR(chain 'B' and (resid 11 through 245 or resid 253 through 863 or resid 866 through 888))BB866 - 888844 - 866

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Components

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


Mass: 98325.352 Da / Num. of mol.: 2 / Fragment: truncated residues 345-375 replaced with GGSGGSG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, KPNB2, MIP1, TRN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92973
#2: Protein RNA-binding protein FUS / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 53623.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUS, TLS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8M Succinic acid pH7.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.36
ReflectionResolution: 4.05→50 Å / Num. obs: 27683 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rpim(I) all: 0.056 / Net I/σ(I): 10.9
Reflection shellResolution: 4.05→4.07 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1301 / CC1/2: 0.596 / Rpim(I) all: 0.472 / % possible all: 95.1

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Processing

Software
NameVersionClassification
phenix.refine1.13_2998refinement
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z5K

2z5k


Resolution: 4.05→41.33 Å / Cross valid method: FREE R-VALUE / σ(F): 66.81 / Phase error: 38.9089
Stereochemistry target values: TWIN_LSQ_F, GeoStd, Monomer Library
RfactorNum. reflection% reflection
Rfree0.2598 1217 5.1 %
Rwork0.2505 22668 -
obs0.3653 23885 87.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.07 Å2
Refinement stepCycle: LAST / Resolution: 4.05→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12966 0 0 0 12966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003613227
X-RAY DIFFRACTIONf_angle_d0.68917933
X-RAY DIFFRACTIONf_chiral_restr0.12092063
X-RAY DIFFRACTIONf_plane_restr0.00592295
X-RAY DIFFRACTIONf_dihedral_angle_d18.13154975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.05-4.230.4264510.44071249X-RAY DIFFRACTION36.84
4.23-4.460.4118980.40972270X-RAY DIFFRACTION67.08
4.46-4.740.39641600.39042990X-RAY DIFFRACTION87.35
4.74-5.10.36011760.34223195X-RAY DIFFRACTION94.33
5.1-5.610.36421530.31553250X-RAY DIFFRACTION95.48
5.61-6.420.31551790.3263247X-RAY DIFFRACTION94.72
6.42-8.070.31531850.32763219X-RAY DIFFRACTION94.37
8.07-35.040.35441870.36743264X-RAY DIFFRACTION93.55

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