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- PDB-1koo: THE CRYSTAL STRUCTURE AND MUTATIONAL ANALYSIS OF A NOVEL RNA-BIND... -

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Basic information

Entry
Database: PDB / ID: 1koo
TitleTHE CRYSTAL STRUCTURE AND MUTATIONAL ANALYSIS OF A NOVEL RNA-BINDING DOMAIN FOUND IN THE HUMAN TAP NUCLEAR MRNA EXPORT FACTOR
ComponentsTIP ASSOCIATING PROTEIN
KeywordsRNA BINDING PROTEIN / mRNA export factor / Constitutive transport element (CTE) / Ribonucleoprotein (RNP) 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 / 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 / cytoplasm / cytosol
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 / 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 / RNA-binding domain superfamily / Leucine-rich repeat 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 / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsHo, D.N. / Coburn, G.A. / Kang, Y. / Cullen, B.R. / Georgiadis, M.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor.
Authors: Ho, D.N. / Coburn, G.A. / Kang, Y. / Cullen, B.R. / Georgiadis, M.M.
#1: Journal: Genes Dev. / Year: 2001
Title: Using viral species specificity to define a critical protein/RNA interaction surface
Authors: Coburn, G.A. / Wiegand, H.L. / Kang, Y. / Ho, D.N. / Georgiadis, M.M. / Cullen, B.R.
#2: Journal: 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
DepositionDec 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)126,0604
Polymers126,0604
Non-polymers00
Water00
1
A: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,5151
Polymers31,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,5151
Polymers31,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,5151
Polymers31,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TIP ASSOCIATING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,5151
Polymers31,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.245, 138.245, 204.998
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: 31514.977 Da / Num. of mol.: 4 / Fragment: RESIDUES 96-372 / Mutation: C252S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / 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: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium potassium tartrate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mg/mlprotein1drop
21.1 Mpotassium/sodium tartrate1reservoir
30.05 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9789 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 13, 2000 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 33824 / Num. obs: 32000 / % possible obs: 84.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 9.8
Reflection shellResolution: 3.8→3.94 Å / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2 / Rsym value: 0.468 / % possible all: 92.5
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 95.5 %
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FT8

1ft8


Resolution: 3.8→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.395 828 -RANDOM
Rwork0.317 ---
all-33395 --
obs-28342 84.9 %-
Refinement stepCycle: LAST / Resolution: 3.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 0 0 6832
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.317
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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