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- EMDB-63788: Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-63788
TitleCryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4
Map data
Sample
  • Complex: The complex of human UBA1-UBE2O-Ub
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 1
    • Protein or peptide: (E3-independent) E2 ubiquitin-conjugating enzyme
    • Protein or peptide: Polyubiquitin-C
  • Ligand: ADENOSINE MONOPHOSPHATE
Keywordscryo-EM / UBA1 / UBE2O / Ubiquitin / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / retrograde transport, endosome to Golgi / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein K63-linked ubiquitination / Maturation of protein E / Maturation of protein E ...E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / retrograde transport, endosome to Golgi / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein K63-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / Regulation of NF-kappa B signaling / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Stabilization of p53 / Negative regulation of FGFR2 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / Negative regulation of FGFR4 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Degradation of AXIN / Regulation of TNFR1 signaling / EGFR downregulation / Termination of translesion DNA synthesis / Hh mutants are degraded by ERAD
Similarity search - Function
: / : / : / UBE2O, ubiquitin binding SH3-C domain / UBE2O, N-terminal SH3-A domain / UBE2O, tandem tSH3-B domain / : / UBE2O, SH3-B domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. ...: / : / : / UBE2O, ubiquitin binding SH3-C domain / UBE2O, N-terminal SH3-A domain / UBE2O, tandem tSH3-B domain / : / UBE2O, SH3-B domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-like modifier-activating enzyme 1 / (E3-independent) E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsChen P-T / Wu K-P
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-110-L03 Taiwan
Academia Sinica (Taiwan)AS-GCS-113-L05 Taiwan
CitationJournal: To Be Published
Title: Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4
Authors: Chen P-T / Wu K-P
History
DepositionMar 17, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63788.png

Downloads & links

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Map

FileDownload / File: emd_63788.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 432 pix.
= 279.936 Å		0.65 Å/pix.
x 432 pix.
= 279.936 Å		0.65 Å/pix.
x 432 pix.
= 279.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.40459877 - 0.60333115
Average (Standard dev.)0.00006136141 (±0.010175488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 279.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63788_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_63788_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of human UBA1-UBE2O-Ub

EntireName: The complex of human UBA1-UBE2O-Ub
Components
  • Complex: The complex of human UBA1-UBE2O-Ub
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 1
    • Protein or peptide: (E3-independent) E2 ubiquitin-conjugating enzyme
    • Protein or peptide: Polyubiquitin-C
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: The complex of human UBA1-UBE2O-Ub

SupramoleculeName: The complex of human UBA1-UBE2O-Ub / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitin-like modifier-activating enzyme 1

MacromoleculeName: Ubiquitin-like modifier-activating enzyme 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.976609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSSPLSKKR RVSGPDPKPG SNCSPAQSVL SEVPSVPTNG MAKNGSEADI DEGLYSRQLY VLGHEAMKRL QTSSVLVSGL RGLGVEIAK NIILGGVKAV TLHDQGTAQW ADLSSQFYLR EEDIGKNRAE VSQPRLAELN SYVPVTAYTG PLVEDFLSGF Q VVVLTNTP ...String:
MSSSPLSKKR RVSGPDPKPG SNCSPAQSVL SEVPSVPTNG MAKNGSEADI DEGLYSRQLY VLGHEAMKRL QTSSVLVSGL RGLGVEIAK NIILGGVKAV TLHDQGTAQW ADLSSQFYLR EEDIGKNRAE VSQPRLAELN SYVPVTAYTG PLVEDFLSGF Q VVVLTNTP LEDQLRVGEF CHNRGIKLVV ADTRGLFGQL FCDFGEEMIL TDSNGEQPLS AMVSMVTKDN PGVVTCLDEA RH GFESGDF VSFSEVQGMV ELNGNQPMEI KVLGPYTFSI CDTSNFSDYI RGGIVSQVKV PKKISFKSLV ASLAEPDFVV TDF AKFSRP AQLHIGFQAL HQFCAQHGRP PRPRNEEDAA ELVALAQAVN ARALPAVQQN NLDEDLIRKL AYVAAGDLAP INAF IGGLA AQEVMKACSG KFMPIMQWLY FDALECLPED KEVLTEDKCL QRQNRYDGQV AVFGSDLQEK LGKQKYFLVG AGAIG CELL KNFAMIGLGC GEGGEIIVTD MDTIEKSNLN RQFLFRPWDV TKLKSDTAAA AVRQMNPHIR VTSHQNRVGP DTERIY DDD FFQNLDGVAN ALDNVDARMY MDRRCVYYRK PLLESGTLGT KGNVQVVIPF LTESYSSSQD PPEKSIPICT LKNFPNA IE HTLQWARDEF EGLFKQPAEN VNQYLTDPKF VERTLRLAGT QPLEVLEAVQ RSLVLQRPQT WADCVTWACH HWHTQYSN N IRQLLHNFPP DQLTSSGAPF WSGPKRCPHP LTFDVNNPLH LDYVMAAANL FAQTYGLTGS QDRAAVATFL QSVQVPEFT PKSGVKIHVS DQELQSANAS VDDSRLEELK ATLPSPDKLP GFKMYPIDFE KDDDSNFHMD FIVAASNLRA ENYDIPSADR HKSKLIAGK IIPAIATTTA AVVGLVCLEL YKVVQGHRQL DSYKNGFLNL ALPFFGFSEP LAAPRHQYYN QEWTLWDRFE V QGLQPNGE EMTLKQFLDY FKTEHKLEIT MLSQGVSMLY SFFMPAAKLK ERLDQPMTEI VSRVSKRKLG RHVRALVLEL CC NDESGED VEVPYVRYTI R

UniProtKB: Ubiquitin-like modifier-activating enzyme 1

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Macromolecule #2: (E3-independent) E2 ubiquitin-conjugating enzyme

MacromoleculeName: (E3-independent) E2 ubiquitin-conjugating enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: (E3-independent) E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 141.554172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADPAAPTPA APAPAQAPAP APEAVPAPAA APVPAPAPAS DSASGPSSDF GPEAGSQRLL FSHDLVSGRY RGSVHFGLVR LIHGEDSDS EGEEEGRGSS GCSEAGGAGH EEGRASPLRR GYVRVQWYPE GVKQHVKETK LKLEDRSVVP RDVVRHMRST D SQCGTVID ...String:
MADPAAPTPA APAPAQAPAP APEAVPAPAA APVPAPAPAS DSASGPSSDF GPEAGSQRLL FSHDLVSGRY RGSVHFGLVR LIHGEDSDS EGEEEGRGSS GCSEAGGAGH EEGRASPLRR GYVRVQWYPE GVKQHVKETK LKLEDRSVVP RDVVRHMRST D SQCGTVID VNIDCAVKLI GTNCIIYPVN SKDLQHIWPF MYGDYIAYDC WLGKVYDLKN QIILKLSNGA RCSMNTEDGA KL YDVCPHV SDSGLFFDDS YGFYPGQVLI GPAKIFSSVQ WLSGVKPVLS TKSKFRVVVE EVQVVELKVT WITKSFCPGG TDS VSPPPS VITQENLGRV KRLGCFDHAQ RQLGERCLYV FPAKVEPAKI AWECPEKNCA QGEGSMAKKV KRLLKKQVVR IMSC SPDTQ CSRDHSMEDP DKKGESKTKS EAESASPEET PDGSASPVEM QDEGAEEPHE AGEQLPPFLL KEGRDDRLHS AEQDA DDEA ADDTDDTSSV TSSASSTTSS QSGSGTSRKK SIPLSIKNLK RKHKRKKNKI TRDFKPGDRV AVEVVTTMTS ADVMWQ DGS VECNIRSNDL FPVHHLDNNE FCPGDFVVDK RVQSCPDPAV YGVVQSGDHI GRTCMVKWFK LRPSGDDVEL IGEEEDV SV YDIADHPDFR FRTTDIVIRI GNTEDGAPHK EDEPSVGQVA RVDVSSKVEV VWADNSKTII LPQHLYNIES EIEESDYD S VEGSTSGASS DEWEDDSDSW ETDNGLVEDE HPKIEEPPIP PLEQPVAPED KGVVISEEAA TAAVQGAVAM AAPMAGLME KAGKDGPPKS FRELKEAIKI LESLKNMTVE QLLTGSPTSP TVEPEKPTRE KKFLDDIKKL QENLKKTLDN VAIVEEEKME AVPDVERKE DKPEGQSPVK AEWPSETPVL CQQCGGKPGV TFTSAKGEVF SVLEFAPSNH SFKKIEFQPP EAKKFFSTVR K EMALLATS LPEGIMVKTF EDRMDLFSAL IKGPTRTPYE DGLYLFDIQL PNIYPAVPPH FCYLSQCSGR LNPNLYDNGK VC VSLLGTW IGKGTERWTS KSSLLQVLIS IQGLILVNEP YYNEAGFDSD RGLQEGYENS RCYNEMALIR VVQSMTQLVR RPP EVFEQE IRQHFSTGGW RLVNRIESWL ETHALLEKAQ ALPNGVPKAS SSPEPPAVAE LSDSGQQEPE DGGPAPGEAS QGSD SEGGA QSLASASRDH TDQTSETAPD ASVPPSVKPK KRRKSYRSFL PEKSGYPDIG FPLFPLSKGF IKSIRGVLTQ FRAAL LEAG MPECTEDK

UniProtKB: (E3-independent) E2 ubiquitin-conjugating enzyme

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Macromolecule #3: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.663908 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SMQIFVKTLT GKTITLEVEP SDTIENVKAK IQDKEGIPPD QQRLIFAGKQ LEDGRTLSDY NIQKESTLHL VLRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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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

Concentration1.3 mg/mL
BufferpH: 7.6
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6dc6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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