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- EMDB-63938: Oligomer structure of a glycosyltransferase -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63938
TitleOligomer structure of a glycosyltransferase
Map data
Sample
  • Complex: glycosyltransferase
    • Protein or peptide: Procollagen galactosyltransferase 1
  • Ligand: GALACTOSE-URIDINE-5'-DIPHOSPHATE
  • Ligand: MANGANESE (II) ION
Keywordsglycosyltransferase / TRANSFERASE
Function / homology
Function and homology information


procollagen galactosyltransferase / procollagen galactosyltransferase activity / positive regulation of collagen fibril organization / Collagen biosynthesis and modifying enzymes / protein O-linked glycosylation / collagen fibril organization / endoplasmic reticulum lumen / membrane
Similarity search - Function
Glycosyltransferase family 25, N-terminal / Glycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / : / Endoplasmic reticulum targeting sequence. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Procollagen galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYu HJ / Zhang M / Sun HH / Liu XT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Oligomer structure of a glycosyltransferase
Authors: Yu HJ / Zhang M / Sun HH / Liu XT
History
DepositionMar 24, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63938.png

Downloads & links

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Map

FileDownload / File: emd_63938.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.24 Å		1.08 Å/pix.
x 240 pix.
= 258.24 Å		1.08 Å/pix.
x 240 pix.
= 258.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.09378291 - 0.1552775
Average (Standard dev.)0.000041071824 (±0.0049809217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63938_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_63938_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 : glycosyltransferase

EntireName: glycosyltransferase
Components
  • Complex: glycosyltransferase
    • Protein or peptide: Procollagen galactosyltransferase 1
  • Ligand: GALACTOSE-URIDINE-5'-DIPHOSPHATE
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: glycosyltransferase

SupramoleculeName: glycosyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Procollagen galactosyltransferase 1

MacromoleculeName: Procollagen galactosyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: procollagen galactosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.566598 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: ERWSPESPLQ APRVLIALLA RNAAHALPTT LGALERLRHP RERTALWVAT DHNMDNTSTV LREWLVAVKS LYHSVEWRPA EEPRSYPDE EGPKHWSDSR YEHVMKLRQA ALKSARDMWA DYILFVDADN LILNPDTLSL LIAENKTVVA PMLDSRAAYS N FWCGMTSQ ...String:
ERWSPESPLQ APRVLIALLA RNAAHALPTT LGALERLRHP RERTALWVAT DHNMDNTSTV LREWLVAVKS LYHSVEWRPA EEPRSYPDE EGPKHWSDSR YEHVMKLRQA ALKSARDMWA DYILFVDADN LILNPDTLSL LIAENKTVVA PMLDSRAAYS N FWCGMTSQ GYYKRTPAYI PIRKRDRRGC FAVPMVHSTF LIDLRKAASR NLAFYPPHPD YTWSFDDIIV FAFSCKQAEV QM YVCNKEE YGFLPVPLRA HSTLQDEAES FMHVQLEVMV KHPPAEPSRF ISAPTKTPDK MGFDEVFMIN LRRRQDRRER MLR ALQAQE IECRLVEAVD GKAMNTSQVE ALGIQMLPGY RDPYHGRPLT KGELGCFLSH YNIWKEVVDR GLQKSLVFED DLRF EIFFK RRLMNLMRDV EREGLDWDLI YVGRKRMQVE HPEKAVPRVR NLVEADYSYW TLAYVISLQG ARKLLAAEPL SKMLP VDEF LPVMFDKHPV SEYKAHFSLR NLHAFSVEPL LIYPTH

UniProtKB: Procollagen galactosyltransferase 1

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Macromolecule #2: GALACTOSE-URIDINE-5'-DIPHOSPHATE

MacromoleculeName: GALACTOSE-URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: GDU
Molecular weightTheoretical: 566.302 Da
Chemical component information

ChemComp-GDU:
GALACTOSE-URIDINE-5'-DIPHOSPHATE

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Macromolecule #3: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MN
Molecular weightTheoretical: 54.938 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 375486
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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