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- PDB-4wyk: Structure of the LRR and NTF2-like domains of NXF1 complexed with NXT1 -

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Basic information

Entry
Database: PDB / ID: 4wyk
TitleStructure of the LRR and NTF2-like domains of NXF1 complexed with NXT1
Components
  • NTF2-related export protein 1
  • Nuclear RNA export factor 1
KeywordsTRANSPORT PROTEIN / nuclear export
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 / cytoplasm / cytosol
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 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 / Resolution: 3.4 Å
AuthorsAibara, S. / Valkov, E. / Stewart, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105178939 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA.
Authors: Aibara, S. / Katahira, J. / Valkov, E. / Stewart, M.
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Nuclear RNA export factor 1
B: NTF2-related export protein 1
C: Nuclear RNA export factor 1
D: NTF2-related export protein 1


Theoretical massNumber of molelcules
Total (without water)135,6284
Polymers135,6284
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13990 Å2
ΔGint-72 kcal/mol
Surface area44250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.046, 83.972, 108.233
Angle α, β, γ (deg.)108.69, 99.76, 97.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nuclear RNA export factor 1 / Tip-associated protein / Tip-associating protein / mRNA export factor TAP


Mass: 52085.277 Da / Num. of mol.: 2 / Fragment: UNP residues 96-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NXF1, TAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU9
#2: Protein NTF2-related export protein 1 / Protein p15


Mass: 15728.561 Da / Num. of mol.: 2 / Fragment: UNP residues 2-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NXT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKK6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 9 % PEG 6000, 1 M LiCl, 0.1 M sodium citrate buffer pH 5.1 See publication for full details.
PH range: 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.4→46.411 Å / Num. obs: 19892 / % possible obs: 93.5 % / Redundancy: 3.9 % / Net I/σ(I): 6.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementResolution: 3.4→46.411 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 1014 5.11 %
Rwork0.2131 --
obs0.2158 19852 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→46.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7679 0 0 0 7679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047820
X-RAY DIFFRACTIONf_angle_d0.79110579
X-RAY DIFFRACTIONf_dihedral_angle_d13.3572933
X-RAY DIFFRACTIONf_chiral_restr0.0311200
X-RAY DIFFRACTIONf_plane_restr0.0031376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.57920.39491270.3152661X-RAY DIFFRACTION93
3.5792-3.80330.33961420.28642785X-RAY DIFFRACTION96
3.8033-4.09680.30341650.24532716X-RAY DIFFRACTION95
4.0968-4.50880.25821470.19872692X-RAY DIFFRACTION94
4.5088-5.16050.24191410.17682517X-RAY DIFFRACTION87
5.1605-6.49890.24971530.20962806X-RAY DIFFRACTION97
6.4989-46.41570.21091390.17062661X-RAY DIFFRACTION92

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