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Open data
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Basic information
Entry | Database: PDB / ID: 5cll | ||||||
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Title | Truncated Ran wild type in complex with GDP-BeF and RanBD1 | ||||||
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![]() | HYDROLASE / GTPase / nuclear transport / Ran binding protein | ||||||
Function / homology | ![]() cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear pore cytoplasmic filaments / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / Nuclear Pore Complex (NPC) Disassembly ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear pore cytoplasmic filaments / 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 / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / 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 / nucleocytoplasmic transport / MicroRNA (miRNA) biogenesis / centrosome localization / Viral Messenger RNA Synthesis / DNA metabolic process / dynein intermediate chain binding / regulation of gluconeogenesis / 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 / Regulation of HSF1-mediated heat shock response / sperm flagellum / mRNA transport / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / ribosomal subunit export from nucleus / 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 / HCMV Late Events / G protein activity / 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 / positive regulation of protein import into nucleus / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / GDP binding / Signaling by ALK fusions and activated point mutants / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vetter, I.R. / Brucker, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.2 KB | Display | ![]() |
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PDB format | ![]() | 220.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ciqC ![]() 5citC ![]() 5ciwC ![]() 5cj2C ![]() 5clqC ![]() 1rrpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() References: UniProt: P49792, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Non-polymers , 4 types, 39 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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