+Open data
-Basic information
Entry | Database: PDB / ID: 7yxx | ||||||
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Title | Cryo-EM structure of USP9X | ||||||
Components | Probable ubiquitin carboxyl-terminal hydrolase FAF-X | ||||||
Keywords | HYDROLASE / USP9X / Deubiquitinase / ubiquitin / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information cytosolic ciliogenesis / K11-linked deubiquitinase activity / positive regulation of TORC2 signaling / protein import into peroxisome matrix, receptor recycling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / female gamete generation / co-SMAD binding / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity ...cytosolic ciliogenesis / K11-linked deubiquitinase activity / positive regulation of TORC2 signaling / protein import into peroxisome matrix, receptor recycling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / female gamete generation / co-SMAD binding / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity / DNA alkylation repair / axon extension / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / RHOV GTPase cycle / protein deubiquitination / RHOU GTPase cycle / cilium assembly / BMP signaling pathway / cysteine-type peptidase activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transforming growth factor beta receptor signaling pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / chromosome segregation / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / neuron migration / regulation of circadian rhythm / cilium / rhythmic process / protein localization / cell migration / positive regulation of protein binding / growth cone / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / amyloid fibril formation / protein stabilization / Ub-specific processing proteases / protein ubiquitination / Amyloid fiber formation / cell division / cysteine-type endopeptidase activity / centrosome / negative regulation of transcription by RNA polymerase II / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Deme, J.C. / Halabelian, L. / Arrowsmith, C.H. / Lea, S.M. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of USP9X Authors: Halabelian, L. / Deme, J.C. / Lea, S.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7yxx.cif.gz | 967.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yxx.ent.gz | 764.6 KB | Display | PDB format |
PDBx/mmJSON format | 7yxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yxx_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7yxx_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7yxx_validation.xml.gz | 149.4 KB | Display | |
Data in CIF | 7yxx_validation.cif.gz | 224.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/7yxx ftp://data.pdbj.org/pub/pdb/validation_reports/yx/7yxx | HTTPS FTP |
-Related structure data
Related structure data | 14368MC 7yxyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 293878.844 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP9X, DFFRX, FAM, USP9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q93008, ubiquitinyl hydrolase 1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: trimer of USP9X / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 56.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330000 / Symmetry type: POINT | ||||||||||||||||||||||||
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