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- EMDB-14369: Cryo-EM structure of USP9X, local refinement of monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-14369
TitleCryo-EM structure of USP9X, local refinement of monomer
Map datasharpened map
Sample
  • Organelle or cellular component: USP9X monomer
    • Protein or peptide: Probable ubiquitin carboxyl-terminal hydrolase FAF-X
KeywordsUSP9X / Deubiquitinase / ubiquitin / Structural Genomics / Structural Genomics Consortium / SGC / HYDROLASE
Function / homology
Function and homology information


cytosolic ciliogenesis / K11-linked deubiquitinase activity / protein import into peroxisome matrix, receptor recycling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / positive regulation of TORC2 signaling / deubiquitinase activity / DNA alkylation repair ...cytosolic ciliogenesis / K11-linked deubiquitinase activity / protein import into peroxisome matrix, receptor recycling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / positive regulation of TORC2 signaling / deubiquitinase activity / DNA alkylation repair / axon extension / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / RHOV GTPase cycle / RHOU GTPase cycle / molecular sequestering activity / cilium assembly / protein deubiquitination / BMP signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transforming growth factor beta receptor signaling pathway / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / chromosome segregation / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / regulation of circadian rhythm / regulation of protein stability / neuron migration / positive regulation of protein binding / rhythmic process / intracellular protein localization / cell migration / growth cone / amyloid fibril formation / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cilium / Amyloid fiber formation / cell division / cysteine-type endopeptidase activity / centrosome / negative regulation of transcription by RNA polymerase II / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin carboxyl-terminal hydrolases, Ubiquitin-like 1 / 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 carboxyl-terminal hydrolases, Ubiquitin-like 1 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDeme JC / Halabelian L
Funding support United States, 1 items
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 JC / Lea SM / Arrowsmith CH / Structural Genomics Consortium (SGC)
History
DepositionFeb 16, 2022-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.323
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.323
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7yxy
  • Surface level: 0.323
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7yxy
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_14369.png

Downloads & links

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Map

FileDownload / File: emd_14369.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.323 / Movie #1: 0.323
Minimum - Maximum-1.2208824 - 3.4015057
Average (Standard dev.)0.0020779022 (±0.044843618)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 372.73602 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z372.736372.736372.736
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-1.2213.4020.002

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Supplemental data

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Mask #1

Fileemd_14369_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_14369_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_14369_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_14369_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : USP9X monomer

EntireName: USP9X monomer
Components
  • Organelle or cellular component: USP9X monomer
    • Protein or peptide: Probable ubiquitin carboxyl-terminal hydrolase FAF-X

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Supramolecule #1: USP9X monomer

SupramoleculeName: USP9X monomer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Probable ubiquitin carboxyl-terminal hydrolase FAF-X

MacromoleculeName: Probable ubiquitin carboxyl-terminal hydrolase FAF-X / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 293.878844 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHSSG RENLYFQGMT ATTRGSPVGG NDNQGQAPDG QSQPPLQQNQ TSSPDSSNEN SPATPPDEQG QGDAPPQLED EEPAFPHTD LAKLDDMINR PRWVVPVLPK GELEVLLEAA IDLSKKGLDV KSEACQRFFR DGLTISFTKI LTDEAVSGWK F EIHRCIIN ...String:
MHHHHHHSSG RENLYFQGMT ATTRGSPVGG NDNQGQAPDG QSQPPLQQNQ TSSPDSSNEN SPATPPDEQG QGDAPPQLED EEPAFPHTD LAKLDDMINR PRWVVPVLPK GELEVLLEAA IDLSKKGLDV KSEACQRFFR DGLTISFTKI LTDEAVSGWK F EIHRCIIN NTHRLVELCV AKLSQDWFPL LELLAMALNP HCKFHIYNGT RPCESVSSSV QLPEDELFAR SPDPRSPKGW LV DLLNKFG TLNGFQILHD RFINGSALNV QIIAALIKPF GQCYEFLTLH TVKKYFLPII EMVPQFLENL TDEELKKEAK NEA KNDALS MIIKSLKNLA SRVPGQEETV KNLEIFRLKM ILRLLQISSF NGKMNALNEV NKVISSVSYY THRHGNPEEE EWLT AERMA EWIQQNNILS IVLRDSLHQP QYVEKLEKIL RFVIKEKALT LQDLDNIWAA QAGKHEAIVK NVHDLLAKLA WDFSP EQLD HLFDCFKASW TNASKKQREK LLELIRRLAE DDKDGVMAHK VLNLLWNLAH SDDVPVDIMD LALSAHIKIL DYSCSQ DRD TQKIQWIDRF IEELRTNDKW VIPALKQIRE ICSLFGEAPQ NLSQTQRSPH VFYRHDLINQ LQHNHALVTL VAENLAT YM ESMRLYARDH EDYDPQTVRL GSRYSHVQEV QERLNFLRFL LKDGQLWLCA PQAKQIWKCL AENAVYLCDR EACFKWYS K LMGDEPDLDP DINKDFFESN VLQLDPSLLT ENGMKCFERF FKAVNCREGK LVAKRRAYMM DDLELIGLDY LWRVVIQSN DDIASRAIDL LKEIYTNLGP RLQVNQVVIH EDFIQSCFDR LKASYDTLCV LDGDKDSVNC ARQEAVRMVR VLTVLREYIN ECDSDYHEE RTILPMSRAF RGKHLSFVVR FPNQGRQVDD LEVWSHTNDT IGSVRRCILN RIKANVAHTK IELFVGGELI D PADDRKLI GQLNLKDKSL ITAKLTQISS NMPSSPDSSS DSSTGSPGNH GNHYSDGPNP EVESCLPGVI MSLHPRYISF LW QVADLGS SLNMPPLRDG ARVLMKLMPP DSTTIEKLRA ICLDHAKLGE SSLSPSLDSL FFGPSASQVL YLTEVVYALL MPA GAPLAD DSSDFQFHFL KSGGLPLVLS MLTRNNFLPN ADMETRRGAY LNALKIAKLL LTAIGYGHVR AVAEACQPGV EGVN PMTQI NQVTHDQAVV LQSALQSIPN PSSECMLRNV SVRLAQQISD EASRYMPDIC VIRAIQKIIW ASGCGSLQLV FSPNE EITK IYEKTNAGNE PDLEDEQVCC EALEVMTLCF ALIPTALDAL SKEKAWQTFI IDLLLHCHSK TVRQVAQEQF FLMCTR CCM GHRPLLFFIT LLFTVLGSTA RERAKHSGDY FTLLRHLLNY AYNSNINVPN AEVLLNNEID WLKRIRDDVK RTGETGI EE TILEGHLGVT KELLAFQTSE KKFHIGCEKG GANLIKELID DFIFPASNVY LQYMRNGELP AEQAIPVCGS PPTINAGF E LLVALAVGCV RNLKQIVDSL TEMYYIGTAI TTCEALTEWE YLPPVGPRPP KGFVGLKNAG ATCYMNSVIQ QLYMIPSIR NGILAIEGTG SDVDDDMSGD EKQDNESNVD PRDDVFGYPQ QFEDKPALSK TEDRKEYNIG VLRHLQVIFG HLAASRLQYY VPRGFWKQF RLWGEPVNLR EQHDALEFFN SLVDSLDEAL KALGHPAMLS KVLGGSFADQ KICQGCPHRY ECEESFTTLN V DIRNHQNL LDSLEQYVKG DLLEGANAYH CEKCNKKVDT VKRLLIKKLP PVLAIQLKRF DYDWERECAI KFNDYFEFPR EL DMEPYTV AGVAKLEGDN VNPESQLIQQ SEQSESETAG STKYRLVGVL VHSGQASGGH YYSYIIQRNG GDGERNRWYK FDD GDVTEC KMDDDEEMKN QCFGGEYMGE VFDHMMKRMS YRRQKRWWNA YILFYERMDT IDQDDELIRY ISELAITTRP HQII MPSAI ERSVRKQNVQ FMHNRMQYSM EYFQFMKKLL TCNGVYLNPP PGQDHLLPEA EEITMISIQL AARFLFTTGF HTKKV VRGS ASDWYDALCI LLRHSKNVRF WFAHNVLFNV SNRFSEYLLE CPSAEVRGAF AKLIVFIAHF SLQDGPCPSP FASPGP SSQ AYDNLSLSDH LLRAVLNLLR REVSEHGRHL QQYFNLFVMY ANLGVAEKTQ LLKLSVPATF MLVSLDEGPG PPIKYQY AE LGKLYSVVSQ LIRCCNVSSR MQSSINGNPP LPNPFGDPNL SQPIMPIQQN VADILFVRTS YVKKIIEDCS NSEETVKL L RFCCWENPQF SSTVLSELLW QVAYSYTYEL RPYLDLLLQI LLIEDSWQTH RIHNALKGIP DDRDGLFDTI QRSKNHYQK RAYQCIKCMV ALFSNCPVAY QILQGNGDLK RKWTWAVEWL GDELERRPYT GNPQYTYNNW SPPVQSNETS NGYFLERSHS ARMTLAKAC ELCPEEEPDD QDAPDEHESP PPEDAPLYPH SPGSQYQQNN HVHGQPYTGP AAHHMNNPQR TGQRAQENYE G SEEVSPPQ TKDQDYKDDD K

UniProtKB: Ubiquitin carboxyl-terminal hydrolase 9X

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 330000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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