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- EMDB-52316: USP1-UAF1 bound to Lys63-linked diubiquitin -

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Basic information

Entry
Database: EMDB / ID: EMD-52316
TitleUSP1-UAF1 bound to Lys63-linked diubiquitin
Map data
Sample
  • Complex: USP1-UAF1 bound to Lys63-linked diubiquitin
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
    • Protein or peptide: WD repeat-containing protein 48
    • Protein or peptide: Polyubiquitin-B
  • Protein or peptide: Polyubiquitin-B
  • Ligand: ZINC ION
KeywordsUSP1 / deubiquitinating enzyme / cysteine protease / complex / HYDROLASE
Function / homology
Function and homology information


regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / monoubiquitinated protein deubiquitination / deubiquitinase activator activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / skeletal system morphogenesis / positive regulation of protein monoubiquitination / fat pad development ...regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / monoubiquitinated protein deubiquitination / deubiquitinase activator activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / skeletal system morphogenesis / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / skin development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / homeostasis of number of cells / protein deubiquitination / single fertilization / embryonic organ development / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / response to UV / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / positive regulation of epithelial cell proliferation / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / skeletal system development / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of receptor signaling pathway via JAK-STAT / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation
Similarity search - Function
WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / : / 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 ...WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / : / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 1 / Polyubiquitin-B / WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsKeijzer N / Sakoltchik J / Sixma TK
Funding support Netherlands, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)TOP714.016.002 Netherlands
Health-HollandLSHM21048-H045 Netherlands
CitationJournal: To Be Published
Title: USP1-UAF1 bound to Lys63-linked diubiquitin
Authors: Keijzer N / Sixma TK / Sakoltchik J
History
DepositionDec 11, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52316.png

Downloads & links

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Map

FileDownload / File: emd_52316.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0192
Minimum - Maximum-0.34302434 - 0.5805047
Average (Standard dev.)0.000013237443 (±0.0099755805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52316_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52316_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : USP1-UAF1 bound to Lys63-linked diubiquitin

EntireName: USP1-UAF1 bound to Lys63-linked diubiquitin
Components
  • Complex: USP1-UAF1 bound to Lys63-linked diubiquitin
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
    • Protein or peptide: WD repeat-containing protein 48
    • Protein or peptide: Polyubiquitin-B
  • Protein or peptide: Polyubiquitin-B
  • Ligand: ZINC ION

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Supramolecule #1: USP1-UAF1 bound to Lys63-linked diubiquitin

SupramoleculeName: USP1-UAF1 bound to Lys63-linked diubiquitin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitin carboxyl-terminal hydrolase 1

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 1 / 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: 91.785992 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHDYDI PTTENLYFQG AMGNRLSLKF FQKKETKRAL DFTDSQENEE KASEYRASEI DQVVPAAQSS PINCEKRENL LPFVGLNNL GNTCYLNSIL QVLYFCPGFK SGVKHLFNII SRKKEALKDE ANQKDKGNCK EDSLASYELI CSLQSLIISV E QLQASFLL ...String:
HHHHHHDYDI PTTENLYFQG AMGNRLSLKF FQKKETKRAL DFTDSQENEE KASEYRASEI DQVVPAAQSS PINCEKRENL LPFVGLNNL GNTCYLNSIL QVLYFCPGFK SGVKHLFNII SRKKEALKDE ANQKDKGNCK EDSLASYELI CSLQSLIISV E QLQASFLL NPEKYTDELA TQPRRLLNTL RELNPMYEGY LQHDAQEVLQ CILGNIQETC QLLKKEEVKN VAELPTKVEE IP HPKEEMN GINSIEMDSM RHSEDFKEKL PKGNGKRKSD TEFGNMKKKV KLSKEHQSLE ENQRQTRSKR KATSDTLESP PKI IPKYIS ENESPRPSQK KSRVKINWLK SATKQPSILS KFCSLGKITT NQGVKGQSKE NECDPEEDLG KCESDNTTNG CGLE SPGNT VTPVNVNEVK PINKGEEQIG FELVEKLFQG QLVLRTRCLE CESLTERRED FQDISVPVQE DELSKVEESS EISPE PKTE MKTLRWAISQ FASVERIVGE DKYFCENCHH YTEAERSLLF DKMPEVITIH LKCFAASGLE FDCYGGGLSK INTPLL TPL KLSLEEWSTK PTNDSYGLFA VVMHSGITIS SGHYTASVKV TDLNSLELDK GNFVVDQMCE IGKPEPLNEE EARGVVE NY NDEEVSIRVG GNTQPSKVLN KKNVEAIGLL AAQKSKADYE LYNKASNPDK VASTAFAENR NSETSDTTGT HESDRNKE S SDQTGINISG FENKISYVVQ SLKEYEGKWL LFDDSEVKVT EEKDFLNSLS PSTSPTSTPY LLFYKKLERP LSNLEPAVS RHAVPSLSRS TRG

UniProtKB: Ubiquitin carboxyl-terminal hydrolase 1

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Macromolecule #2: WD repeat-containing protein 48

MacromoleculeName: WD repeat-containing protein 48 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.130719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WSHPQFEKGA LEVLFQGPGM AAHHRQNTAG RRKVQVSYVI RDEVEKYNRN GVNALQLDPA LNRLFTAGRD SIIRIWSVNQ HKQDPYIAS MEHHTDWVND IVLCCNGKTL ISASSDTTVK VWNAHKGFCM STLRTHKDYV KALAYAKDKE LVASAGLDRQ I FLWDVNTL ...String:
WSHPQFEKGA LEVLFQGPGM AAHHRQNTAG RRKVQVSYVI RDEVEKYNRN GVNALQLDPA LNRLFTAGRD SIIRIWSVNQ HKQDPYIAS MEHHTDWVND IVLCCNGKTL ISASSDTTVK VWNAHKGFCM STLRTHKDYV KALAYAKDKE LVASAGLDRQ I FLWDVNTL TALTASNNTV TTSSLSGNKD SIYSLAMNQL GTIIVSGSTE KVLRVWDPRT CAKLMKLKGH TDNVKALLLN RD GTQCLSG SSDGTIRLWS LGQQRCIATY RVHDEGVWAL QVNDAFTHVY SGGRDRKIYC TDLRNPDIRV LICEEKAPVL KME LDRSAD PPPAIWVATT KSTVNKWTLK GIHNFRASGD YDNDCTNPIT PLCTQPDQVI KGGASIIQCH ILNDKRHILT KDTN NNVAY WDVLKACKVE DLGKVDFEDE IKKRFKMVYV PNWFSVDLKT GMLTITLDES DCFAAWVSAK DAGFSSPDGS DPKLN LGGL LLQALLEYWP RTHVNPMDEE ENEVNHVNGE QENRVQKGNG YFQVPPHTPV IFGEAGGRTL FRLLCRDSGG ETESML LNE TVPQWVIDIT VDKNMPKFNK IPFYLQPHAS SGAKTLKKDR LSASDMLQVR KVMEHVYEKI INLDNESQTT SSSNNEK PG EQEKEEDIAV LAEEKIELLC QDQVLDPNMD LRTVKHFIWK SGGDLTLHYL RSPRNSRHAV PSLSRSTRGS

UniProtKB: WD repeat-containing protein 48

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Macromolecule #3: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.604884 KDa
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG(ABU)

UniProtKB: Polyubiquitin-B

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Macromolecule #4: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.54777 KDa
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQ(DAB)ESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHepesHepes
150.0 mMNaClsodium chloride
2.0 mMTCEPTris(2-carboxyethyl)phosphine hydrochloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
DetailsCollected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5833 / Average exposure time: 2.71 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 10500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3110350
Startup modelType of model: OTHER
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299304
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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