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- PDB-1yrg: THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATIN... -

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Basic information

Entry
Database: PDB / ID: 1yrg
TitleTHE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN
ComponentsGTPASE-ACTIVATING PROTEIN RNA1_SCHPO
KeywordsTRANSCRIPTION / GTPASE-ACTIVATING PROTEIN / GAP / RNA1P / RANGAP / LRR / LEUCINE-RICH REPEAT PROTEIN / TWINNING / HEMIHEDRAL TWINNING / MEROHEDRAL TWINNING / MEROHEDRY
Function / homology
Function and homology information


SUMOylation of nuclear envelope proteins / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / small GTPase-mediated signal transduction / nuclear periphery / GTPase activator activity / positive regulation of protein export from nucleus / small GTPase binding / perinuclear region of cytoplasm / nucleus ...SUMOylation of nuclear envelope proteins / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / small GTPase-mediated signal transduction / nuclear periphery / GTPase activator activity / positive regulation of protein export from nucleus / small GTPase binding / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Leucine rich repeat, ribonuclease inhibitor type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.66 Å
AuthorsHillig, R.C. / Renault, L. / Vetter, I.R. / Drell, T. / Wittinghofer, A. / Becker, J.
Citation
Journal: Mol.Cell / Year: 1999
Title: The crystal structure of rna1p: a new fold for a GTPase-activating protein.
Authors: Hillig, R.C. / Renault, L. / Vetter, I.R. / Drell 4th, T. / Wittinghofer, A. / Becker, J.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: RNA1 encodes a GTPase-activating protein specific for Gsp1p, the Ran/TC4 homologue of Saccharomyces cerevisiae.
Authors: Becker, J. / Melchior, F. / Gerke, V. / Bischoff, F.R. / Ponstingl, H. / Wittinghofer, A.
#2: Journal: Mol.Biol.Cell / Year: 1993
Title: A functional homologue of the RNA1 gene product in Schizosaccharomyces pombe: purification, biochemical characterization, and identification of a leucine-rich repeat motif.
Authors: Melchior, F. / Weber, K. / Gerke, V.
History
DepositionMar 29, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Jan 22, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _citation.pdbx_database_id_DOI / _citation_author.name
Revision 1.6Dec 27, 2023Group: 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: GTPASE-ACTIVATING PROTEIN RNA1_SCHPO
B: GTPASE-ACTIVATING PROTEIN RNA1_SCHPO


Theoretical massNumber of molelcules
Total (without water)86,2832
Polymers86,2832
Non-polymers00
Water37821
1
A: GTPASE-ACTIVATING PROTEIN RNA1_SCHPO


Theoretical massNumber of molelcules
Total (without water)43,1411
Polymers43,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPASE-ACTIVATING PROTEIN RNA1_SCHPO


Theoretical massNumber of molelcules
Total (without water)43,1411
Polymers43,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.530, 175.530, 55.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Cell settingtetragonal
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99602, 0.08914, 0.00232), (0.08915, 0.99601, 0.0046), (-0.0019, 0.00479, -0.99999)
Vector: 75.57918, -3.78333, 47.4025)

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Components

#1: Protein GTPASE-ACTIVATING PROTEIN RNA1_SCHPO / RNA1P / RANGAP / GTPASE-ACTIVATING PROTEIN FOR SPI1 / THE S.POMBE ORTHOLOGUE OF RAN


Mass: 43141.461 Da / Num. of mol.: 2 / Mutation: SER2ALA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Description: SELENOMETHIONINE MUTANT EXPRESSED IN E.COLI B834
Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P41391
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ELEVEN LEUCINE-RICH REPEATS (LRR) OF S.POMBE RNA1P: LRR1(2-32), LRR2(33-60), LRR3(61-94), ...THE ELEVEN LEUCINE-RICH REPEATS (LRR) OF S.POMBE RNA1P: LRR1(2-32), LRR2(33-60), LRR3(61-94), LRR4(95-122), LRR5 (123-159), LRR6(160-187), LRR7(188-216), LRR8(217-244), LRR9(245-274),LRR10(275-303),LRR11(304-333).
Sequence detailsMET1 CLEAVED OFF; MUTATION SER2ALA DUE TO EXPRESSION SYSTEM

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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: 2.49 Å3/Da / Density % sol: 50.3 %
Description: DATA SHOWED HEMIHEDRAL TWINNING. INTENSITIES WERE DE-TEWINNED FOR STRUCTURE DETERMINATION
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROPS MADE FROM 2-4 MICROLITER OF PROTEIN SOLUTION (25 MG/ML RNA1P IN 0.02 M TRIS-HCL, 0.002 M DTE, PH 7.5) AND THE SAME VOLUME OF RESERVOIR SOLUTION (21-24% PEG 2000 MME, 0.1 M TRIS- ...Details: HANGING DROPS MADE FROM 2-4 MICROLITER OF PROTEIN SOLUTION (25 MG/ML RNA1P IN 0.02 M TRIS-HCL, 0.002 M DTE, PH 7.5) AND THE SAME VOLUME OF RESERVOIR SOLUTION (21-24% PEG 2000 MME, 0.1 M TRIS-HCL, 0.2 M LI2SO4, 0.02 M MGCL2, PH 8.5), VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
121-24 %PEG2000 MME1reservoir
2100 mMTris-HCl1reservoir
3200 mM1reservoirLi2SO4
420 mM1reservoirMgCl2
525 mg/mlprotain1drop
620 mMTris-HCl1drop
72 mMDTE1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.946
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 2.64→20 Å / Num. obs: 24708 / % possible obs: 97.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 34 Å2 / Rsym value: 8.4 / Net I/σ(I): 18.2
Reflection shellResolution: 2.64→2.69 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 19.6 / % possible all: 58.9
Reflection
*PLUS
Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 58.9 % / Rmerge(I) obs: 0.196

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Processing

Software
NameVersionClassification
SOLVEphasing
MLPHAREphasing
SHARPphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.66→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 2684368.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT TARGET: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1215 5.1 %RANDOM
Rwork0.228 ---
obs-23730 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.03 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å20 Å2
2--3.52 Å20 Å2
3----7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-20 Å
Luzzati sigma a0.47 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 0 21 5401
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.66→2.83 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 175 5 %
Rwork0.299 3353 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / % reflection Rfree: 5 % / Rfactor Rwork: 0.299

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