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- PDB-1oai: Complex between Tap UBA domain and FxFG nucleoporin peptide -

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Basic information

Entry
Database: PDB / ID: 1oai
TitleComplex between Tap UBA domain and FxFG nucleoporin peptide
Components
  • FXFG NUCLEOPORIN PEPTIDE
  • NUCLEAR RNA EXPORT FACTOR
KeywordsNUCLEAR TRANSPORT / NUCLEAR TRANSPORT FACTOR / NUCLEOPORIN
Function / homology
Function and homology information


nuclear RNA export factor complex / 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 / nuclear pore / mRNA export from nucleus / cytoplasmic stress granule ...nuclear RNA export factor complex / 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 / nuclear pore / mRNA export from nucleus / 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 / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote ...Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Ubiquitin-associated (UBA) domain / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Helicase, Ruva Protein; domain 3 / Leucine-rich repeat / RNA-binding domain superfamily / Leucine-rich repeat domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear RNA export factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1 Å
AuthorsGrant, R.P. / Neuhaus, D. / Stewart, M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural Basis for the Interaction between the Tap/Nxf1 Uba Domain and Fg Nucleoporins at 1 A Resolution
Authors: Grant, R.P. / Neuhaus, D. / Stewart, M.
History
DepositionJan 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Advisory / Data collection
Category: diffrn_radiation / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEAR RNA EXPORT FACTOR
B: FXFG NUCLEOPORIN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)7,7302
Polymers7,7302
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.974, 42.974, 66.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2027-

HOH

21A-2028-

HOH

31A-2029-

HOH

41B-2006-

HOH

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Components

#1: Protein NUCLEAR RNA EXPORT FACTOR / TAP / TIP ASSOCIATING PROTEIN / MRNA EXPORT FACTOR TAP


Mass: 6797.592 Da / Num. of mol.: 1 / Fragment: UBA DOMAIN, RESIDUES 561-619
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UBU9
#2: Protein/peptide FXFG NUCLEOPORIN PEPTIDE


Mass: 931.967 Da / Num. of mol.: 1 / Fragment: NUCLEOPORIN PEPTIDE, RESIDUES 10-18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.31 Å3/Da / Density % sol: 37.5 %
Crystal growpH: 6.5 / Details: AS DESCRIBED IN MANUSCRIPT, pH 6.50
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMammonium acetate1reservoirpH6.5
21.9 Mammonium sulfate1reservoir
310 mMdithiothreitol1reservoir
41 mMEDTA1reservoir
51.3 mMTap UBA1drop
62.3 mMFxFG peptide1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9393
DetectorType: ASCD / Detector: CCD / Date: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1→24.85 Å / Num. obs: 38728 / % possible obs: 100 % / Redundancy: 5.56 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.334
Reflection shellResolution: 1→1.05 Å / Redundancy: 4.77 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.92 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1 Å / Lowest resolution: 25 Å / Num. obs: 39136 / % possible obs: 100 % / Redundancy: 5.6 % / Num. measured all: 217401
Reflection shell
*PLUS
Highest resolution: 1 Å / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1→6 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.256 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.159 1932 5 %RANDOM
Rwork0.149 ---
obs-36943 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms542 0 0 127 669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021554
X-RAY DIFFRACTIONr_bond_other_d0.0030.02457
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.928742
X-RAY DIFFRACTIONr_angle_other_deg0.88731083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.602566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.275
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02618
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02109
X-RAY DIFFRACTIONr_nbd_refined0.2880.2130
X-RAY DIFFRACTIONr_nbd_other0.2640.2481
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9321.5339
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0142537
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8713215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6114.5205
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.217 113
Rwork0.234 2620
Software
*PLUS
Name: REFMAC / Version: '5.1.24 24/04/2001' / Classification: refinement
Refinement
*PLUS
Highest resolution: 1 Å / Lowest resolution: 6 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.158 / Rfactor Rwork: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.023
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.94
LS refinement shell
*PLUS
Highest resolution: 1.001 Å / Lowest resolution: 1.026 Å / Rfactor Rfree: 0.217 / Num. reflection Rfree: 2620 / Rfactor Rwork: 0.234 / Total num. of bins used: 20

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