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- PDB-1jn5: Structural basis for the recognition of a nucleoporin FG-repeat b... -

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Basic information

Entry
Database: PDB / ID: 1jn5
TitleStructural basis for the recognition of a nucleoporin FG-repeat by the NTF2-like domain of TAP-p15 mRNA export factor
Components
  • FG-repeat
  • TAP
  • p15
KeywordsTRANSPORT PROTEIN / NTF2-like domain / nucleoporin / FG-repeat
Function / homology
Function and homology information


nuclear RNA export factor complex / nuclear pore central transport channel / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore ...nuclear RNA export factor complex / nuclear pore central transport channel / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / protein export from nucleus / small GTPase binding / cytoplasmic stress granule / protein transport / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / Nuclear transport factor 2/Mtr2 / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. ...Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / Nuclear transport factor 2/Mtr2 / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat / Leucine-rich repeat domain superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Nuclear RNA export factor 1 / NTF2-related export protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsFribourg, S. / Braun, I.C. / Izaurralde, E. / Conti, E.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural basis for the recognition of a nucleoporin FG repeat by the NTF2-like domain of the TAP/p15 mRNA nuclear export factor.
Authors: Fribourg, S. / Braun, I.C. / Izaurralde, E. / Conti, E.
History
DepositionJul 23, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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: p15
B: TAP
C: FG-repeat


Theoretical massNumber of molelcules
Total (without water)44,9253
Polymers44,9253
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-28 kcal/mol
Surface area15930 Å2
MethodPISA
2
A: p15

B: TAP
C: FG-repeat


Theoretical massNumber of molelcules
Total (without water)44,9253
Polymers44,9253
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation6_554x-y,x,z-1/61
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-15 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.200, 105.200, 172.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein p15 / NTF2-related export protein 1


Mass: 15859.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKK6
#2: Protein TAP / tip associating protein


Mass: 27987.678 Da / Num. of mol.: 1 / Fragment: residues 371-619
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-CS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBU9
#3: Protein/peptide FG-repeat


Mass: 1077.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.

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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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Na/K Tartrate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
250 mMTris1drop
350 mM1dropNaCl
40.5 mMdithiothreitol1drop
50.8 Msodium potassium tartrate1reservoir
6100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 237824 / Num. obs: 233306 / % possible obs: 98.1 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054
Reflection shellResolution: 2.8→30 Å / Rmerge(I) obs: 0.351 / Rsym value: 0.351 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 14630 / Num. measured all: 233306
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1jkg

1jkg


Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 515 4.05 %RANDOM
Rwork0.241 ---
all-14547 --
obs-12685 87.2 %-
Displacement parametersBiso mean: 14.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 0 0 2555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.42598
X-RAY DIFFRACTIONc_bond_d0.007632
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 3 / % reflection Rfree: 4.05 % / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS

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