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- PDB-1xk5: Crystal structure of the m3G-cap-binding domain of snurportin1 in... -

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Basic information

Entry
Database: PDB / ID: 1xk5
TitleCrystal structure of the m3G-cap-binding domain of snurportin1 in complex with a m3GpppG-cap dinucleotide
Componentssnurportin-1SPN1
KeywordsTRANSPORT PROTEIN / Protein-RNA-complex
Function / homology
Function and homology information


RNA import into nucleus / RNA cap binding / snRNA import into nucleus / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear pore / protein import into nucleus / snRNP Assembly / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / DNA ligase/mRNA capping enzyme / Importin-alpha, importin-beta-binding domain / IBB domain profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TPG / Snurportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsStrasser, A. / Dickmanns, A. / Luehrmann, R. / Ficner, R.
Citation
Journal: Embo J. / Year: 2005
Title: Structural basis for m(3)G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1
Authors: Strasser, A. / Dickmanns, A. / Luehrmann, R. / Ficner, R.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Purification, crystallization and preliminary crystallographic data of the m3G cap-binding domain of human snRNP import factor snurportin 1
Authors: Strasser, A. / Dickmanns, A. / Schmidt, U. / Penka, E. / Urlaub, H. / Sekine, M. / Luehrmann, R. / Ficner, R.
#2: Journal: Embo J. / Year: 1998
Title: Snurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure
Authors: Huber, J. / Cronshagen, U. / Kadokura, M. / Marshallsay, C. / Wada, T. / Sekine, M. / Luehrmann, R.
History
DepositionSep 27, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: snurportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9822
Polymers23,1491
Non-polymers8331
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.470, 57.470, 130.090
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 snurportin-1 / SPN1 / RNA / U transporter 1 / UsnRNPs


Mass: 23149.438 Da / Num. of mol.: 1
Fragment: m3G-cap-binding domain comprising amino acids 97-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O95149
#2: Chemical ChemComp-TPG / 2,2,7-TRIMETHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE


Type: RNA linking / Mass: 832.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H35N10O18P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 8% PEG20K, 100mM MES pH6.0 for initial crystals and 200mM sodium citrate pH5.5 for larger crystals after seeding, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 249994 / Redundancy: 11 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.7
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.4→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.276 449 RANDOM
Rwork0.227 --
all-9065 -
obs-8620 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 54 82 1765
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_mcbond_it0.06
X-RAY DIFFRACTIONx_mcangle_it0.66
X-RAY DIFFRACTIONx_bond_d0.084
X-RAY DIFFRACTIONx_angle_d0.672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.4-2.510.4035430.3211X-RAY DIFFRACTION7306
2.51-2.640.4659650.306X-RAY DIFFRACTION10316
2.64-2.810.3468520.2763X-RAY DIFFRACTION11076
2.81-3.020.3548640.2634X-RAY DIFFRACTION11186
3.02-3.320.3501570.2647X-RAY DIFFRACTION11136
3.32-3.80.2903510.22X-RAY DIFFRACTION11356

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