+Open data
-Basic information
Entry | Database: PDB / ID: 5clq | ||||||
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Title | Ran Y39A in complex with GPPNHP and RanBD1 | ||||||
Components |
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Keywords | HYDROLASE / GTPase / nuclear transport / Ran binding protein | ||||||
Function / homology | Function and homology information cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase activity / SUMO ligase complex / annulate lamellae / nuclear pore cytoplasmic filaments / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly / manchette / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Transferases; Acyltransferases; Aminoacyltransferases / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / dynein intermediate chain binding / regulation of gluconeogenesis / DNA metabolic process / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / protein sumoylation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / Regulation of HSF1-mediated heat shock response / mRNA transport / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / response to amphetamine / centriole / protein export from nucleus / viral process / SUMOylation of chromatin organization proteins / GTPase activator activity / mitotic spindle organization / G protein activity / HCMV Late Events / male germ cell nucleus / RHO GTPases Activate Formins / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Signaling by ALK fusions and activated point mutants / recycling endosome / ISG15 antiviral mechanism / small GTPase binding / positive regulation of protein import into nucleus / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / GDP binding / melanosome / protein folding / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / snRNP Assembly / midbody / actin cytoskeleton organization / nuclear membrane / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 | 5clq.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5clq.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 5clq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/5clq ftp://data.pdbj.org/pub/pdb/validation_reports/cl/5clq | HTTPS FTP |
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-Related structure data
Related structure data | 5ciqC 5citC 5ciwC 5cj2C 5cllC 1rrpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 24364.008 Da / Num. of mol.: 2 / Mutation: Y39A 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: Protein | Mass: 18957.402 Da / Num. of mol.: 2 / Fragment: Ran binding domain 1, UNP residues 1155-1321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP2, NUP358 / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P49792, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Non-polymers , 4 types, 22 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8M ammonium sulfate, 2.5% PEG 1500, 100 mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0039 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2010 |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0039 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→87.924 Å / Num. obs: 19912 / % possible obs: 99.4 % / Redundancy: 6.56 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.99 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 6.87 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2.97 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1rrp Resolution: 3.2→19.984 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.984 Å
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Refine LS restraints |
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LS refinement shell |
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