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- PDB-4fq3: Crystal structure of transportin/FUS-NLS -

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Basic information

Entry
Database: PDB / ID: 4fq3
TitleCrystal structure of transportin/FUS-NLS
Components
  • Fusion (Involved in t(12;16) in malignant liposarcoma)
  • Transportin-1
KeywordsPROTEIN BINDING / transport receptor / Nuclear localization sequence / nucleus
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
RNA-binding protein FUS / 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 ...RNA-binding protein FUS / 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 / Fusion (Involved in t(1216) in malignant liposarcoma) / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGong, W. / Niu, C. / Jia, M. / Gao, F.
CitationJournal: To be Published
Title: Crystal structure of transportin/FUS-NLS
Authors: Gong, W. / Niu, C. / Jia, M. / Gao, F.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 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

Downloads & links

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Assembly

Deposited unit
A: Transportin-1
B: Fusion (Involved in t(12;16) in malignant liposarcoma)


Theoretical massNumber of molelcules
Total (without water)105,3882
Polymers105,3882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-6 kcal/mol
Surface area37110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.811, 158.292, 68.370
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: 101408.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92973
#2: Protein/peptide Fusion (Involved in t(12;16) in malignant liposarcoma)


Mass: 3979.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TBR3, UniProt: P35637*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28971

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.94 Å / SU ML: 0.86 / σ(F): 1.34 / Phase error: 26.45
RfactorNum. reflection% reflection
Rfree0.251 1455 5.1 %
Rwork0.1976 --
obs0.2003 28525 99.33 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.474 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.5127 Å20 Å20 Å2
2--1.2537 Å20 Å2
3---14.2589 Å2
Refinement stepCycle: LAST / Resolution: 3→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 0 0 6776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066957
X-RAY DIFFRACTIONf_angle_d1.069451
X-RAY DIFFRACTIONf_dihedral_angle_d18.5782625
X-RAY DIFFRACTIONf_chiral_restr0.0791079
X-RAY DIFFRACTIONf_plane_restr0.0051220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.40071400.30612671X-RAY DIFFRACTION99
3.1072-3.23140.3371460.26072650X-RAY DIFFRACTION99
3.2314-3.37830.31481400.23852662X-RAY DIFFRACTION100
3.3783-3.55620.30511660.2282666X-RAY DIFFRACTION100
3.5562-3.77860.27021460.20482687X-RAY DIFFRACTION100
3.7786-4.06960.2351350.17822692X-RAY DIFFRACTION100
4.0696-4.4780.18221270.15692719X-RAY DIFFRACTION100
4.478-5.12310.21121600.15772718X-RAY DIFFRACTION100
5.1231-6.4440.28151390.23352744X-RAY DIFFRACTION99
6.444-29.94190.1931560.16892861X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 29.513 Å / Origin y: -38.3402 Å / Origin z: -3.4077 Å
111213212223313233
T-0.4782 Å20.0419 Å20.0091 Å2--0.085 Å20.0165 Å2--0.0648 Å2
L1.2229 °2-0.0689 °20.1856 °2-0.3867 °2-0.1858 °2--0.4139 °2
S0.1849 Å °-0.0001 Å °-0.2564 Å °-0.2205 Å °-0.1844 Å °0.2164 Å °0.2175 Å °-0.207 Å °-0.0291 Å °
Refinement TLS groupSelection details: all

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