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- PDB-1ft8: CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE MRNA EXPORT FA... -

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Basic information

Entry
Database: PDB / ID: 1ft8
TitleCRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE MRNA EXPORT FACTOR TAP
ComponentsTIP ASSOCIATING PROTEIN
KeywordsRNA BINDING PROTEIN / ribonucleoprotein (RNP / RRM / RBD) and leucine-rich-repeat (LRR) domains
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
Nuclear RNA export factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsLiker, E. / Fernandez, E. / Izaurralde, E. / Conti, E.
CitationJournal: EMBO J. / Year: 2000
Title: The structure of the mRNA export factor TAP reveals a cis arrangement of a non-canonical RNP domain and an LRR domain.
Authors: Liker, E. / Fernandez, E. / Izaurralde, E. / Conti, E.
History
DepositionSep 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIP ASSOCIATING PROTEIN
B: TIP ASSOCIATING PROTEIN
C: TIP ASSOCIATING PROTEIN
D: TIP ASSOCIATING PROTEIN
E: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)154,0115
Polymers154,0115
Non-polymers00
Water00
1
A: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,8021
Polymers30,8021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,8021
Polymers30,8021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,8021
Polymers30,8021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,8021
Polymers30,8021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,8021
Polymers30,8021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.918, 139.918, 206.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
TIP ASSOCIATING PROTEIN / TAP


Mass: 30802.217 Da / Num. of mol.: 5 / Fragment: RESIDUES 42-312 / Mutation: C119W,A226V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-CS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU9

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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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, EDTA, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2100 mMcacodylate1reservoir
318 %(w/v)PEG80001reservoir
420 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. all: 227961 / Num. obs: 35832 / % possible obs: 0.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.6
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 6 % / Rmerge(I) obs: 0.28 / % possible all: 99.9
Reflection
*PLUS
% possible obs: 99.6 % / Num. measured all: 227961
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 7

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.15→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.303 1434 random
Rwork0.303 --
all0.303 35989 -
obs0.303 35832 -
Refinement stepCycle: LAST / Resolution: 3.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 0 0 6913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.75

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