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- PDB-7yxy: Cryo-EM structure of USP9X, local refinement of monomer -

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Basic information

Entry
Database: PDB / ID: 7yxy
TitleCryo-EM structure of USP9X, local refinement of monomer
ComponentsProbable ubiquitin carboxyl-terminal hydrolase FAF-X
KeywordsHYDROLASE / 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 deubiquitination involved in ubiquitin-dependent protein catabolic process / protein import into peroxisome matrix, receptor recycling / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity ...cytosolic ciliogenesis / K11-linked deubiquitinase activity / positive regulation of TORC2 signaling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein import into peroxisome matrix, receptor recycling / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity / DNA alkylation repair / protein K63-linked deubiquitination / axon extension / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / RHOV GTPase cycle / protein deubiquitination / RHOU GTPase cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cilium assembly / BMP signaling pathway / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / transforming growth factor beta receptor signaling pathway / chromosome segregation / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / neuron migration / protein localization / regulation of circadian rhythm / cilium / rhythmic process / cell migration / positive regulation of protein binding / growth cone / ubiquitinyl hydrolase 1 / amyloid fibril formation / cysteine-type deubiquitinase activity / 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 / cytoplasm / cytosol
Similarity search - Function
Domain of unknown function DUF3517 / Domain of unknown function (DUF3517) / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Armadillo-type fold
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 9X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDeme, J.C. / Halabelian, L. / Arrowsmith, C.H. / Lea, S.M. / Structural Genomics Consortium (SGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: 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
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Probable ubiquitin carboxyl-terminal hydrolase FAF-X


Theoretical massNumber of molelcules
Total (without water)293,8791
Polymers293,8791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area82590 Å2

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Components

#1: Protein Probable ubiquitin carboxyl-terminal hydrolase FAF-X / Deubiquitinating enzyme FAF-X / Fat facets in mammals / hFAM / Fat facets protein-related / X- ...Deubiquitinating enzyme FAF-X / Fat facets in mammals / hFAM / Fat facets protein-related / X-linked / Ubiquitin thioesterase FAF-X / Ubiquitin-specific protease 9 / X chromosome / Ubiquitin-specific-processing protease FAF-X


Mass: 293878.844 Da / Num. of mol.: 1
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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: USP9X monomer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 56.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314336
ELECTRON MICROSCOPYf_angle_d0.55719393
ELECTRON MICROSCOPYf_dihedral_angle_d4.3061886
ELECTRON MICROSCOPYf_chiral_restr0.0392145
ELECTRON MICROSCOPYf_plane_restr0.0052479

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