+Open data
-Basic information
Entry | Database: PDB / ID: 5vo5 | ||||||
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Title | Crystal structure of Lgd-Shrub complex, single chain fusion | ||||||
Components | Coiled-coil and C2 domain-containing protein 1-like,GH13992p | ||||||
Keywords | TRANSPORT PROTEIN / ESCRT | ||||||
Function / homology | Function and homology information positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / fusome / Macroautophagy / contractile ring / wing disc morphogenesis ...positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / fusome / Macroautophagy / contractile ring / wing disc morphogenesis / compound eye development / female germ-line stem cell asymmetric division / phosphatidylinositol phosphate binding / ESCRT III complex / sensory organ development / proximal dendrite / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / apicolateral plasma membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / dendrite morphogenesis / endosomal transport / neuron remodeling / negative regulation of Notch signaling pathway / mitotic cytokinesis / Notch signaling pathway / multivesicular body / intracellular protein transport / cytoplasmic side of plasma membrane / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell cortex / midbody / endosome membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / symbiont entry into host cell / RNA polymerase II cis-regulatory region sequence-specific DNA binding / neuronal cell body / regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å | ||||||
Authors | McMillan, B.J. / Seegar, T.C.M. / Blacklow, S.C. | ||||||
Citation | Journal: Cell Rep / Year: 2017 Title: Structural Basis for Regulation of ESCRT-III Complexes by Lgd. Authors: McMillan, B.J. / Tibbe, C. / Drabek, A.A. / Seegar, T.C.M. / Blacklow, S.C. / Klein, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vo5.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vo5.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 5vo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vo5_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 5vo5_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | 5vo5_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 5vo5_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/5vo5 ftp://data.pdbj.org/pub/pdb/validation_reports/vo/5vo5 | HTTPS FTP |
-Related structure data
Related structure data | 5vnySC 5j45S 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
#1: Protein | Mass: 20906.725 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: l(2)gd1, lgd, CG4713, shrb, Vps32, CG8055, Dmel_CG8055 Production host: Escherichia coli (E. coli) / References: UniProt: Q9VKJ9, UniProt: Q8T0Q4 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.02 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 18% PEG 3350 0.1 M sodium citrate pH 5.5 Cryopreserved using 20% glycerol, 25% PEG 3350, 0.1 M sodium citrate 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.004→48.97 Å / Num. obs: 27084 / % possible obs: 97.36 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06595 / Net I/σ(I): 11.44 |
Reflection shell | Resolution: 2.004→2.076 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.549 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 1428 / CC1/2: 0.365 / Rpim(I) all: 0.9336 / % possible all: 93.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VNY, 5J45 Resolution: 2.004→48.967 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.004→48.967 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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