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- EMDB-63796: Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1 (B) -

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Basic information

Entry
Database: EMDB / ID: EMD-63796
TitleCryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1 (B)
Map data
Sample
  • Complex: The complex of human UBA1-UBE2O-Ub
    • Protein or peptide: UBA1
    • Protein or peptide: UBE2O
    • Protein or peptide: Ubiquitin
Keywordscryo-EM / UBA1 / UBE2O / Ubiquitin / CYTOSOLIC PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 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 (B)
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_63796.png

Downloads & links

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Map

FileDownload / File: emd_63796.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: 0.038
Minimum - Maximum-0.19105595 - 0.3522473
Average (Standard dev.)-0.00019528884 (±0.00732196)
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: #1

Fileemd_63796_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63796_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: UBA1
    • Protein or peptide: UBE2O
    • Protein or peptide: Ubiquitin

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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: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: UBA1

MacromoleculeName: UBA1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSSPLSKKR RVSGPDPKPG SNCSPAQSVL SEVPSVPTNG MAKNGSEADI DEGLYSRQLY VLGHEAMKRL QTSSVLVSGL RGLGVEIAKN IILGGVKAVT LHDQGTAQWA DLSSQFYLRE EDIGKNRAEV SQPRLAELNS YVPVTAYTGP LVEDFLSGFQ VVVLTNTPLE ...String:
MSSSPLSKKR RVSGPDPKPG SNCSPAQSVL SEVPSVPTNG MAKNGSEADI DEGLYSRQLY VLGHEAMKRL QTSSVLVSGL RGLGVEIAKN IILGGVKAVT LHDQGTAQWA DLSSQFYLRE EDIGKNRAEV SQPRLAELNS YVPVTAYTGP LVEDFLSGFQ VVVLTNTPLE DQLRVGEFCH NRGIKLVVAD TRGLFGQLFC DFGEEMILTD SNGEQPLSAM VSMVTKDNPG VVTCLDEARH GFESGDFVSF SEVQGMVELN GNQPMEIKVL GPYTFSICDT SNFSDYIRGG IVSQVKVPKK ISFKSLVASL AEPDFVVTDF AKFSRPAQLH IGFQALHQFC AQHGRPPRPR NEEDAAELVA LAQAVNARAL PAVQQNNLDE DLIRKLAYVA AGDLAPINAF IGGLAAQEVM KACSGKFMPI MQWLYFDALE CLPEDKEVLT EDKCLQRQNR YDGQVAVFGS DLQEKLGKQK YFLVGAGAIG CELLKNFAMI GLGCGEGGEI IVTDMDTIEK SNLNRQFLFR PWDVTKLKSD TAAAAVRQMN PHIRVTSHQN RVGPDTERIY DDDFFQNLDG VANALDNVDA RMYMDRRCVY YRKPLLESGT LGTKGNVQVV IPFLTESYSS SQDPPEKSIP ICTLKNFPNA IEHTLQWARD EFEGLFKQPA ENVNQYLTDP KFVERTLRLA GTQPLEVLEA VQRSLVLQRP QTWADCVTWA CHHWHTQYSN NIRQLLHNFP PDQLTSSGAP FWSGPKRCPH PLTFDVNNPL HLDYVMAAAN LFAQTYGLTG SQDRAAVATF LQSVQVPEFT PKSGVKIHVS DQELQSANAS VDDSRLEELK ATLPSPDKLP GFKMYPIDFE KDDDSNFHMD FIVAASNLRA ENYDIPSADR HKSKLIAGKI IPAIATTTAA VVGLVCLELY KVVQGHRQLD SYKNGFLNLA LPFFGFSEPL AAPRHQYYNQ EWTLWDRFEV QGLQPNGEEM TLKQFLDYFK TEHKLEITML SQGVSMLYSF FMPAAKLKER LDQPMTEIVS RVSKRKLGRH VRALVLELCC NDESGEDVEV PYVRYTIR

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Macromolecule #2: UBE2O

MacromoleculeName: UBE2O / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VFSVLEFAPS NHSFKKIEFQ PPEAKKFFST VRKEMALLAT SLPEGIMVKT FEDRMDLFSA LIKGPTRTPY EDGLYLFDIQ LPNIYPAVPP HFCYLSQCSG RLNPNLYDNG KVCVSLLGTW IGKGTERWTS KSSLLQVLIS IQGLILVNEP YYNEAGFDSD RGLQEGYENS ...String:
VFSVLEFAPS NHSFKKIEFQ PPEAKKFFST VRKEMALLAT SLPEGIMVKT FEDRMDLFSA LIKGPTRTPY EDGLYLFDIQ LPNIYPAVPP HFCYLSQCSG RLNPNLYDNG KVCVSLLGTW IGKGTERWTS KSSLLQVLIS IQGLILVNEP YYNEAGFDSD RGLQEGYENS RCYNEMALIR VVQSMTQLVR RPPEVFEQEI RQHFSTGGWR LVNRIESWLE THALLEKSGY PDIGFPLFPL SKGFIKSIRG VLTQFRAALL EAGMPECTED K

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Macromolecule #3: Ubiquitin

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

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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: 7.6
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54479
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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