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- PDB-5yvi: Crystal structure of Karyopherin beta2 in complex with FUS(456-526) -

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Basic information

Entry
Database: PDB / ID: 5yvi
TitleCrystal structure of Karyopherin beta2 in complex with FUS(456-526)
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 / nuclear localization sequence binding / membraneless organelle assembly / mRNA stabilization / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / intracellular membraneless organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / nuclear localization sequence binding / membraneless organelle assembly / mRNA stabilization / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / intracellular membraneless organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / postsynaptic cytosol / positive regulation of double-strand break repair via homologous recombination / presynaptic cytosol / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity / molecular condensate scaffold activity / protein homooligomerization / GABA-ergic synapse / small GTPase binding / protein import into nucleus / amyloid fibril formation / transcription coactivator activity / cilium / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / glutamatergic synapse / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
TAF15/EWS/TLS family / 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 / Zinc finger domain ...TAF15/EWS/TLS family / 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 / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / 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: 2.9 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,8862
Polymers105,8862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-3 kcal/mol
Surface area37580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.042, 156.102, 68.248
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: 7561.034 Da / Num. of mol.: 1 / Fragment: C-terminal 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8M Succinic acid

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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 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 36917 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rpim(I) all: 0.049 / Net I/σ(I): 18.8
Reflection shellResolution: 2.73→2.78 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1669 / CC1/2: 0.597 / Rpim(I) all: 0.585 / % possible all: 91.9

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Processing

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

4fdd


Resolution: 2.9→44.904 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.34
RfactorNum. reflection% reflection
Rfree0.2312 1467 5 %
Rwork0.1789 --
obs0.1816 29333 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→44.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6760 0 0 0 6760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086903
X-RAY DIFFRACTIONf_angle_d0.9569366
X-RAY DIFFRACTIONf_dihedral_angle_d23.7122603
X-RAY DIFFRACTIONf_chiral_restr0.0511066
X-RAY DIFFRACTIONf_plane_restr0.0071208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00370.3131090.2442068X-RAY DIFFRACTION70
3.0037-3.12390.26861250.2192382X-RAY DIFFRACTION82
3.1239-3.2660.2941380.21322616X-RAY DIFFRACTION89
3.266-3.43820.26221510.2132867X-RAY DIFFRACTION97
3.4382-3.65350.24261530.18832914X-RAY DIFFRACTION100
3.6535-3.93540.21011560.17112960X-RAY DIFFRACTION100
3.9354-4.33120.20311570.16142964X-RAY DIFFRACTION100
4.3312-4.95720.20251570.15022986X-RAY DIFFRACTION100
4.9572-6.24290.2611580.18853008X-RAY DIFFRACTION99
6.2429-44.90920.20371630.15913101X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 29.4202 Å / Origin y: 40.2364 Å / Origin z: 30.6658 Å
111213212223313233
T0.1945 Å20.0245 Å2-0.0054 Å2-0.1246 Å2-0.0395 Å2--0.1219 Å2
L2.059 °2-0.3232 °20.6575 °2-0.8971 °2-0.6284 °2--0.9416 °2
S0.1075 Å °-0.1431 Å °-0.2601 Å °-0.0677 Å °0.0065 Å °0.1309 Å °0.0724 Å °-0.0633 Å °-0.0598 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 890
2X-RAY DIFFRACTION1allB508 - 526

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