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- PDB-4fdd: Crystal structure of KAP beta2-PY-NLS -

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Basic information

Entry
Database: PDB / ID: 4fdd
TitleCrystal structure of KAP beta2-PY-NLS
Components
  • RNA-binding protein FUS
  • Transportin-1
KeywordsTRANSPORT PROTEIN / HEAT repeats / Karyopherin / nuclear import / protein transport / importin / transportin
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 / cytosol / cytoplasm
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 / molecular replacement / Resolution: 2.3 Å
AuthorsZhang, Z.C. / Chook, Y.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and energetic basis of ALS-causing mutations in the atypical proline-tyrosine nuclear localization signal of the Fused in Sarcoma protein (FUS).
Authors: Zhang, Z.C. / Chook, Y.M.
#1: Journal: Structure / Year: 2007
Title: Conformational heterogeneity of karyopherin beta2 is segmental.
Authors: Cansizoglu, A.E. / Chook, Y.M.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structure-based design of a pathway-specific nuclear import inhibitor.
Authors: Cansizoglu, A.E. / Lee, B.J. / Zhang, Z.C. / Fontoura, B.M. / M Chook, Y.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2006
Title: Rules for nuclear localization sequence recognition by karyopherin beta 2.
Authors: Lee, B.J. / Cansizoglu, A.E. / Louis, T.H. / Zhang, Z.C. / Chook, Y.M.
#4: Journal: Nature / Year: 1999
Title: Structure of the nuclear transport complex karyopherin-beta2-Ran x GppNHp.
Authors: Chook, Y.M. / Blobel, G.
History
DepositionMay 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)99,9192
Polymers99,9192
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-6 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.720, 157.255, 67.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 96622.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB2, MIP1, TNPO1, Transportin-1, TRN / Plasmid: pGexTev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92973
#2: Protein/peptide RNA-binding protein FUS / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 3296.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUS, TLS / Plasmid: pGexTev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35637
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7
Details: 1 M succinic acid, 0.1 M HEPES pH 7.0 and 1% PEG MME 2000, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→99.61 Å / Num. obs: 60461 / % possible obs: 97.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.074 / Χ2: 1.2 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3430.45324200.857178.9
2.34-2.383.20.43226390.923186.8
2.38-2.433.40.40828460.944192.8
2.43-2.4840.38629561.019197.8
2.48-2.534.50.36930251.072198.6
2.53-2.595.10.34130501.135199.4
2.59-2.665.50.30630251.238199.5
2.66-2.735.80.26830701.256199.8
2.73-2.8160.23630811.348199.7
2.81-2.96.10.20930371.444199.7
2.9-36.30.17730661.347199.7
3-3.126.50.15130791.475199.6
3.12-3.266.60.12430661.445199.9
3.26-3.446.80.10831071.432199.9
3.44-3.6570.09230981.17199.8
3.65-3.937.10.0831191.0631100
3.93-4.337.10.07131031.252199.9
4.33-4.957.10.07131541.094199.9
4.95-6.2470.06931901.113199.9
6.24-506.70.03933300.766199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.8 Å
Translation3 Å49.8 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→99.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU B: 16.74 / SU ML: 0.182 / SU R Cruickshank DPI: 0.2382 / SU Rfree: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 3061 5.1 %RANDOM
Rwork0.2078 ---
all0.2796 ---
obs0.287 60430 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.87 Å2 / Biso mean: 70.672 Å2 / Biso min: 26.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2--0.37 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→99.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6821 0 0 148 6969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026967
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9769457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9345853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.99824.984317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.894151249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8221536
X-RAY DIFFRACTIONr_chiral_restr0.0930.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215220
LS refinement shellResolution: 2.297→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 157 -
Rwork0.365 3279 -
all-3436 -
obs--78.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5613-0.114-0.07270.35670.12770.05140.0960.01810.0708-0.027-0.0814-0.0525-0.0101-0.0084-0.01470.0480.02470.00740.14040.03630.076134.84538.096-3.742
22.87150.46390.45131.81190.15680.10170.061-0.00540.12940.1183-0.02380.07680.0003-0.0267-0.03720.0835-0.01410.03850.16350.05410.136733.51742.6884.661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 890
2X-RAY DIFFRACTION2B507 - 526

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