+Open data
-Basic information
Entry | Database: PDB / ID: 5ciq | ||||||
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Title | Ran GDP wild type tetragonal crystal form | ||||||
Components | GTP-binding nuclear protein Ran | ||||||
Keywords | HYDROLASE / GTPase / nuclear transport / transport protein | ||||||
Function / homology | Function and homology information 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 ...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 / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / dynein intermediate chain binding / DNA metabolic process / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / nuclear pore / centriole / protein export from nucleus / viral process / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Vetter, I.R. / Brucker, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy. Authors: Rudack, T. / Jenrich, S. / Brucker, S. / Vetter, I.R. / Gerwert, K. / Kotting, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ciq.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ciq.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ciq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/5ciq ftp://data.pdbj.org/pub/pdb/validation_reports/ci/5ciq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24456.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET3d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG 1000, 50 mM TRIS pH 8, 20 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2009 |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→34.23 Å / Num. all: 52073 / Num. obs: 52073 / % possible obs: 98.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.11 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.0585 / Mean I/σ(I) obs: 2.05 / % possible all: 85.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: human Ran GDP Resolution: 1.65→34.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.218 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→34.23 Å
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