+Open data
-Basic information
Entry | Database: PDB / ID: 1k5d | ||||||
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Title | Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN/SIGNALING ACTIVATOR / RAN / RANBP1 / RANGAP / GAP / SIGNAL TRANSDUCTION / NUCLEAR TRANSPORT / GTP HYDROLYSIS / GROUND STATE / COMPLEX (GTP-BINDING-GTPASE ACTIVATION) / SIGNALING PROTEIN-SIGNALING ACTIVATOR COMPLEX | ||||||
Function / homology | Function and homology information SUMOylation of nuclear envelope proteins / positive regulation of mitotic centrosome separation / Postmitotic nuclear pore complex (NPC) reformation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding ...SUMOylation of nuclear envelope proteins / positive regulation of mitotic centrosome separation / Postmitotic nuclear pore complex (NPC) reformation / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / GDP-dissociation inhibitor activity / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / small GTPase-mediated signal transduction / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / sperm flagellum / nuclear pore / protein export from nucleus / centriole / viral process / nuclear periphery / GTPase activator activity / mitotic spindle organization / G protein activity / positive regulation of protein export from nucleus / male germ cell nucleus / hippocampus development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / centrosome / chromatin binding / chromatin / GTP binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / signal transduction / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Seewald, M.J. / Koerner, C. / Wittinghofer, A. / Vetter, I.R. | ||||||
Citation | Journal: Nature / Year: 2002 Title: RanGAP mediates GTP hydrolysis without an arginine finger. Authors: Seewald, M.J. / Korner, C. / Wittinghofer, A. / Vetter, I.R. #1: Journal: Science / Year: 1997 Title: THE RAS-RASGAP COMPLEX: STRUCTURAL BASIS FOR GTPASE ACTIVATION AND ITS LOSS IN ONCOGENIC RAS MUTANTS Authors: Scheffzek, K. / Ahmadian, M.R. / Kabsch, W. / Wiesmueller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A. #2: Journal: Nature / Year: 1999 Title: STRUCTURE OF A RAN-BINDING DOMAIN COMPLEXED WITH RAN BOUND TO A GTP ANALOGUE: IMPLICATIONS FOR NUCLEAR TRANSPORT Authors: Vetter, I.R. / Nowak, C. / Nishimoto, T. / Kuhlmann, J. / Wittinghofer, A. #3: 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, T. / Wittinghofer, A. / Becker, J. #4: 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. #5: Journal: J.Biol.Chem. / Year: 1997 Title: THE ACIDIC C-TERMINAL DOMAIN OF RNA1P IS REQUIRED FOR THE BINDING OF RAN.GTP AND FOR RANGAP ACTIVITY Authors: Haberland, J. / Becker, J. / Gerke, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k5d.cif.gz | 517.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k5d.ent.gz | 426.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k5d ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k5d | HTTPS FTP |
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-Related structure data
Related structure data | 1k5gC 1yrgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 3 types, 12 molecules ADGJBEHKCFIL
#1: Protein | Mass: 24456.105 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62826 #2: Protein | Mass: 23352.199 Da / Num. of mol.: 4 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43487 #3: Protein | Mass: 43272.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Plasmid: PET3D / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P41391 |
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-Non-polymers , 3 types, 350 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GNP / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.39 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 9, 2000 / Details: MICROFOCUS BEAMLINE, 30 MICROMETER APERTURE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 163530 / Num. obs: 163530 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 72.1 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.7→2.87 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 409414 |
Reflection shell | *PLUS % possible obs: 97.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YRG Resolution: 2.7→20 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber (CNS 1.0) Details: SOME OF THE RESIDUES HAVE WEAK DENSITY, PLEASE CHECK B FACTORS.
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Solvent computation | Solvent model: flat model / Bsol: 44.7494 Å2 / ksol: 0.320174 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.238 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 61.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.42 / % reflection Rfree: 10 % / Rfactor Rwork: 0.39 |