[English] 日本語
Yorodumi
- EMDB-63798: Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63798
TitleCryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1
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: Ubiquitin
  • 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 / hypothalamus gonadotrophin-releasing hormone neuron development / retrograde transport, endosome to Golgi / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule ...E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / retrograde transport, endosome to Golgi / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / seminiferous tubule development / female gonad development / ubiquitin conjugating enzyme activity / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein monoubiquitination / protein K63-linked ubiquitination / neuron projection morphogenesis / energy homeostasis / 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 / 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 / regulation of neuron apoptotic process / 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 / positive regulation of protein ubiquitination / 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 / regulation of mitochondrial membrane potential / 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
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-B / 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: 3.42 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 -Recruitment state 1
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

-
Structure visualization

Supplemental images

emd_63798.png

Downloads & links

-
Map

FileDownload / File: emd_63798.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
AxesX (Sec.)Y (Row.)Z (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: 3.95
Minimum - Maximum-22.531442999999999 - 49.633167
Average (Standard dev.)-0.0013198091 (±0.98232394)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
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: Ubiquitin
  • Ligand: ADENOSINE MONOPHOSPHATE

-
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)

-
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

-
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: 30.865404 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VFSVLEFAPS NHSFKKIEFQ PPEAKKFFST VRKEMALLAT SLPEGIMVKT FEDRMDLFSA LIKGPTRTPY EDGLYLFDIQ LPNIYPAVP PHFCYLSQCS GRLNPNLYDN GKVCVSLLGT WIGKGTERWT SKSSLLQVLI SIQGLILVNE PYYNEAGFDS D RGLQEGYE ...String:
VFSVLEFAPS NHSFKKIEFQ PPEAKKFFST VRKEMALLAT SLPEGIMVKT FEDRMDLFSA LIKGPTRTPY EDGLYLFDIQ LPNIYPAVP PHFCYLSQCS GRLNPNLYDN GKVCVSLLGT WIGKGTERWT SKSSLLQVLI SIQGLILVNE PYYNEAGFDS D RGLQEGYE NSRCYNEMAL IRVVQSMTQL VRRPPEVFEQ EIRQHFSTGG WRLVNRIESW LETHALLEKS GYPDIGFPLF PL SKGFIKS IRGVLTQFRA ALLEAGMPEC TEDK

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

-
Macromolecule #3: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114055
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more