+Open data
-Basic information
Entry | Database: PDB / ID: 5cll | ||||||
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Title | Truncated Ran wild type in complex with GDP-BeF 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 / DNA metabolic process / NLS-bearing protein import into nucleus / regulation of gluconeogenesis / dynein intermediate chain binding / SUMOylation of ubiquitinylation proteins / ribosomal subunit export from nucleus / Vpr-mediated nuclear import of PICs / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / SUMOylation of DNA replication proteins / protein sumoylation / Signaling by ALK fusions and activated point mutants / ribosomal large subunit export from nucleus / Regulation of HSF1-mediated heat shock response / sperm flagellum / mRNA transport / 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 / 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 / recycling endosome / ISG15 antiviral mechanism / small GTPase binding / HCMV Early Events / positive regulation of protein import into nucleus / protein import into nucleus / Separation of Sister Chromatids / GDP binding / melanosome / protein folding / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / snRNP Assembly / midbody / actin cytoskeleton organization / nuclear membrane / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / chromatin Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 5cll.cif.gz | 272.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cll.ent.gz | 220.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/5cll ftp://data.pdbj.org/pub/pdb/validation_reports/cl/5cll | HTTPS FTP |
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-Related structure data
Related structure data | 5ciqC 5citC 5ciwC 5cj2C 5clqC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 21729.260 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: Protein | Mass: 18957.402 Da / Num. of mol.: 2 / Fragment: Ran binding domain 1, 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, 39 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 18 % PEG 4000, 250 mM ammonium sulfate, 100 mM MES pH 6.25, 1 mM BeF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 21, 2014 |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.446→46.806 Å / Num. obs: 24587 / % possible obs: 95.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.17 |
Reflection shell | Resolution: 2.446→2.51 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.291 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1rrp Resolution: 2.45→46.806 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.89 / SU B: 22.852 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.91 / ESU R Free: 0.327 / 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: 38.385 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→46.806 Å
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Refine LS restraints |
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