+Open data
-Basic information
Entry | Database: PDB / ID: 3gj7 | ||||||
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Title | Crystal structure of human RanGDP-Nup153ZnF12 complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / G protein / GDP / Ran / Nup153 / nuclear pore / Zinc Finger / Acetylation / Cytoplasm / GTP-binding / Host-virus interaction / Isopeptide bond / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Protein transport / Transport / Ubl conjugation / DNA-binding / Metal-binding / mRNA transport / Nuclear pore complex / Translocation / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins ...nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / negative regulation of RNA export from nucleus / annulate lamellae / Regulation of HSF1-mediated heat shock response / nuclear pore complex assembly / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / nuclear inclusion body / nuclear pore nuclear basket / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / nuclear localization sequence binding / dynein intermediate chain binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / mRNA transport / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / protein-membrane adaptor activity / centriole / viral process / protein export from nucleus / nuclear periphery / 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 / small GTPase binding / 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 / double-stranded DNA binding / nuclear membrane / 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 / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Partridge, J.R. / Schwartz, T.U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystallographic and Biochemical Analysis of the Ran-binding Zinc Finger Domain. Authors: Partridge, J.R. / Schwartz, T.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gj7.cif.gz | 218.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gj7.ent.gz | 170.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/3gj7 ftp://data.pdbj.org/pub/pdb/validation_reports/gj/3gj7 | HTTPS FTP |
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-Related structure data
Related structure data | 3gj0C 3gj3SC 3gj4C 3gj5C 3gj6C 3gj8C 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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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: 24846.479 Da / Num. of mol.: 2 / Mutation: F35S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3)-RIL / References: UniProt: P62826 #2: Protein | Mass: 10143.563 Da / Num. of mol.: 2 Fragment: Nup153 - Zinc finger module 12: UNP residues 658-750 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nup153 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3)-RIL / References: UniProt: P49791 |
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-Non-polymers , 4 types, 304 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #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: 2.05 Å3/Da / Density % sol: 39.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 18-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 39224 / Num. obs: 39224 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 37.56 Å2 / Rsym value: 0.06 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.16 / Rsym value: 0.4 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GJ3 Resolution: 1.93→29.752 Å / SU ML: 0.41 / Phase error: 26.81 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.845 Å2 / ksol: 0.311 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→29.752 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: Chain D |