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- PDB-3rw6: Structure of nuclear RNA export factor TAP bound to CTE RNA -

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Basic information

Entry
Database: PDB / ID: 3rw6
TitleStructure of nuclear RNA export factor TAP bound to CTE RNA
Components
  • Nuclear RNA export factor 1
  • constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA
KeywordsTRANSPORT PROTEIN/RNA / retroviral constitutive transport element (CTE) / RNA recognition motif (RRM) / leucine-rich repeat (LRR) motif / TRANSPORT PROTEIN-RNA complex
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 / mRNA export from nucleus / nuclear pore / 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 / mRNA export from nucleus / nuclear pore / 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 / 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 RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / 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 RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / UBA-like superfamily / RRM (RNA recognition motif) domain / NTF2-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Nuclear RNA export factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTeplova, M. / Khin, N.W. / Patel, D.J. / Izaurralde, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure-function studies of nucleocytoplasmic transport of retroviral genomic RNA by mRNA export factor TAP.
Authors: Teplova, M. / Wohlbold, L. / Khin, N.W. / Izaurralde, E. / Patel, D.J.
History
DepositionMay 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
H: constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA
F: constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA
B: Nuclear RNA export factor 1


Theoretical massNumber of molelcules
Total (without water)101,5904
Polymers101,5904
Non-polymers00
Water2,432135
1
A: Nuclear RNA export factor 1
H: constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA


Theoretical massNumber of molelcules
Total (without water)50,7952
Polymers50,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-8 kcal/mol
Surface area21940 Å2
MethodPISA
2
F: constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA
B: Nuclear RNA export factor 1


Theoretical massNumber of molelcules
Total (without water)50,7952
Polymers50,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-5 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.412, 117.048, 84.773
Angle α, β, γ (deg.)90.000, 106.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30509.930 Da / Num. of mol.: 2 / Fragment: unp residues 96-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NXF1, TAP, TAP (NXF1) / Plasmid: T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBU9
#2: RNA chain constitutive transport element(CTE)of Mason-Pfizer monkey virus RNA


Mass: 20284.963 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: enzymatic synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 2 M ammonium acetate, 0.1 M Na acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 44640 / % possible obs: 96.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.074 / Χ2: 1.03 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.382.90.23142040.869192.3
2.38-2.483.10.20743071.011193.3
2.48-2.593.40.18143301.033194.2
2.59-2.733.70.16144211.04195.7
2.73-2.94.20.12944671.035197.1
2.9-3.124.90.09645261.069197.9
3.12-3.445.50.07945761.049199.1
3.44-3.936.10.07145991.053199.4
3.93-4.956.60.06246081.004199.4
4.95-506.90.06346021.042197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RW7 and an idealized A-form RNA 7-nt duplex

3rw7


Resolution: 2.3→37.866 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.37 / σ(F): 0.09 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 2256 5.06 %
Rwork0.2033 --
obs0.2059 44618 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.263 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso max: 125.6 Å2 / Biso mean: 48.4009 Å2 / Biso min: 19.26 Å2
Baniso -1Baniso -2Baniso -3
1-21.0013 Å2-0 Å21.5355 Å2
2---14.034 Å2-0 Å2
3----6.9673 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 2680 0 135 6774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077046
X-RAY DIFFRACTIONf_angle_d1.33810138
X-RAY DIFFRACTIONf_chiral_restr0.0681235
X-RAY DIFFRACTIONf_plane_restr0.004830
X-RAY DIFFRACTIONf_dihedral_angle_d21.7192815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2966-2.34650.40231120.35482454256690
2.3465-2.40110.38921510.32882524267593
2.4011-2.46110.37261420.30962498264093
2.4611-2.52760.31031320.2952612274494
2.5276-2.6020.32321390.28522584272395
2.602-2.6860.35691240.28742628275296
2.686-2.78190.35711350.27242654278996
2.7819-2.89330.29841480.25112656280498
2.8933-3.02490.30641460.24072673281998
3.0249-3.18430.28651560.20862668282498
3.1843-3.38370.24871200.20452763288399
3.3837-3.64480.22711500.18182722287299
3.6448-4.01120.18461540.161227202874100
4.0112-4.59080.22081570.14922738289599
4.5908-5.78060.21420.14092742288499
5.7806-37.87120.19541480.14332726287497

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