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- PDB-5yvh: Crystal structure of Karyopherin beta2 in complex with FUS(371-526) -

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Basic information

Entry
Database: PDB / ID: 5yvh
TitleCrystal structure of Karyopherin beta2 in complex with FUS(371-526)
Components
  • RNA-binding protein FUS
  • Transportin-1
KeywordsPROTEIN TRANSPORT/RNA BINDING PROTEIN / Importin family / TRANSPORT PROTEIN / 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 / 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
RNA-binding protein FUS / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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
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: RNA-binding protein FUS


Theoretical massNumber of molelcules
Total (without water)114,3092
Polymers114,3092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-5 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.425, 156.532, 67.822
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: 98325.352 Da / Num. of mol.: 1 / 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: 15983.178 Da / Num. of mol.: 1 / Fragment: Arg/Gly-rich domain
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: 3.01 Å3/Da / Density % sol: 59.07 %
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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 25064 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rpim(I) all: 0.051 / Net I/av σ(I): 11.99 / Net I/σ(I): 5.4
Reflection shellResolution: 3.15→3.2 Å / Mean I/σ(I) obs: 1.34 / CC1/2: 0.68 / Rpim(I) all: 0.533

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDD

4fdd


Resolution: 3.15→41.355 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.49
RfactorNum. reflection% reflection
Rfree0.2624 1071 4.99 %
Rwork0.213 --
obs0.2155 21445 87.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→41.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6621 0 0 0 6621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086760
X-RAY DIFFRACTIONf_angle_d1.169167
X-RAY DIFFRACTIONf_dihedral_angle_d16.0882553
X-RAY DIFFRACTIONf_chiral_restr0.071045
X-RAY DIFFRACTIONf_plane_restr0.0081179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.29330.3577450.275861X-RAY DIFFRACTION30
3.2933-3.46690.28441140.25562179X-RAY DIFFRACTION76
3.4669-3.6840.30841410.2292670X-RAY DIFFRACTION93
3.684-3.96820.26751520.2152876X-RAY DIFFRACTION100
3.9682-4.36710.24131520.19242883X-RAY DIFFRACTION100
4.3671-4.99810.24521530.1912912X-RAY DIFFRACTION100
4.9981-6.29350.26481550.22832951X-RAY DIFFRACTION100
6.2935-41.35860.24521590.20483042X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 29.5799 Å / Origin y: 41.2374 Å / Origin z: 30.2869 Å
111213212223313233
T0.6133 Å20.0101 Å2-0.0054 Å2-0.5301 Å2-0.0499 Å2--0.3952 Å2
L2.1981 °2-0.3987 °20.7041 °2-1.2165 °2-0.7015 °2--1.0144 °2
S0.0827 Å °-0.1829 Å °-0.2062 Å °-0.0982 Å °0.0218 Å °0.1388 Å °0.0939 Å °-0.0651 Å °-0.0856 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 889
2X-RAY DIFFRACTION1allB508 - 526

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