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- EMDB-60075: Human lysine O-link glycosylation complex, LH3/ColGalT1 with boun... -

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Basic information

Entry
Database: EMDB / ID: EMD-60075
TitleHuman lysine O-link glycosylation complex, LH3/ColGalT1 with bound UDP-galactose
Map data
Sample
  • Complex: A protein modification complex bound with co-substrate
    • Protein or peptide: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
    • Protein or peptide: Procollagen galactosyltransferase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-OXOGLUTARIC ACID
  • Ligand: FE (II) ION
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: MANGANESE (II) ION
  • Ligand: GALACTOSE-URIDINE-5'-DIPHOSPHATE
Keywordscomplex / hydroxylase / glycosyltransferase / ER protein / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase / procollagen galactosyltransferase activity / positive regulation of collagen fibril organization / basement membrane assembly ...procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase / procollagen galactosyltransferase activity / positive regulation of collagen fibril organization / basement membrane assembly / epidermis morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / endothelial cell morphogenesis / protein O-linked glycosylation / L-ascorbic acid binding / collagen fibril organization / neural tube development / lung morphogenesis / small molecule binding / rough endoplasmic reticulum / trans-Golgi network / vasodilation / protein localization / collagen-containing extracellular matrix / in utero embryonic development / iron ion binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / membrane / metal ion binding
Similarity search - Function
Glycosyl transferase family 2 / Glycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily ...Glycosyl transferase family 2 / Glycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Endoplasmic reticulum targeting sequence. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 / Procollagen galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsPeng J / Li W / Yao D / Xia Y / Wang Q / Cai Y / Li S / Cao M / Shen Y / Ma P ...Peng J / Li W / Yao D / Xia Y / Wang Q / Cai Y / Li S / Cao M / Shen Y / Ma P / Liao R / Qin A / Cao Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072468 China
National Natural Science Foundation of China (NSFC)82272519 China
CitationJournal: Nat Commun / Year: 2025
Title: The structural basis for the human procollagen lysine hydroxylation and dual-glycosylation.
Authors: Junjiang Peng / Wenguo Li / Deqiang Yao / Ying Xia / Qian Wang / Yan Cai / Shaobai Li / Mi Cao / Yafeng Shen / Peixiang Ma / Rijing Liao / Jie Zhao / An Qin / Yu Cao /
Abstract: The proper assembly and maturation of collagens necessitate the orchestrated hydroxylation and glycosylation of multiple lysyl residues in procollagen chains. Dysfunctions in this multistep ...The proper assembly and maturation of collagens necessitate the orchestrated hydroxylation and glycosylation of multiple lysyl residues in procollagen chains. Dysfunctions in this multistep modification process can lead to severe collagen-associated diseases. To elucidate the coordination of lysyl processing activities, we determine the cryo-EM structures of the enzyme complex formed by LH3/PLOD3 and GLT25D1/ColGalT1, designated as the KOGG complex. Our structural analysis reveals a tetrameric complex comprising dimeric LH3/PLOD3s and GLT25D1/ColGalT1s, assembled with interactions involving the N-terminal loop of GLT25D1/ColGalT1 bridging another GLT25D1/ColGalT1 and LH3/PLOD3. We further elucidate the spatial configuration of the hydroxylase, galactosyltransferase, and glucosyltransferase sites within the KOGG complex, along with the key residues involved in substrate binding at these enzymatic sites. Intriguingly, we identify a high-order oligomeric pattern characterized by the formation of a fiber-like KOGG polymer assembled through the repetitive incorporation of KOGG tetramers as the biological unit.
History
DepositionMay 9, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60075.png

Downloads & links

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Map

FileDownload / File: emd_60075.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-2.168819 - 4.0534725
Average (Standard dev.)0.00061738834 (±0.055690244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60075_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_60075_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : A protein modification complex bound with co-substrate

EntireName: A protein modification complex bound with co-substrate
Components
  • Complex: A protein modification complex bound with co-substrate
    • Protein or peptide: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
    • Protein or peptide: Procollagen galactosyltransferase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-OXOGLUTARIC ACID
  • Ligand: FE (II) ION
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: MANGANESE (II) ION
  • Ligand: GALACTOSE-URIDINE-5'-DIPHOSPHATE

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Supramolecule #1: A protein modification complex bound with co-substrate

SupramoleculeName: A protein modification complex bound with co-substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Multifunctional procollagen lysine hydroxylase and glycosyltransf...

MacromoleculeName: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: procollagen-lysine 5-dioxygenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.776031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE GYLRFLRSAE FFNYTVRTLG LGEEWRGGDV ARTVGGGQK VRWLKKEMEK YADREDMIIM FVDSYDVILA GSPTELLKKF VQSGSRLLFS AESFCWPEWG LAEQYPEVGT G KRFLNSGG ...String:
MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE GYLRFLRSAE FFNYTVRTLG LGEEWRGGDV ARTVGGGQK VRWLKKEMEK YADREDMIIM FVDSYDVILA GSPTELLKKF VQSGSRLLFS AESFCWPEWG LAEQYPEVGT G KRFLNSGG FIGFATTIHQ IVRQWKYKDD DDDQLFYTRL YLDPGLREKL SLNLDHKSRI FQNLNGALDE VVLKFDRNRV RI RNVAYDT LPIVVHGNGP TKLQLNYLGN YVPNGWTPEG GCGFCNQDRR TLPGGQPPPR VFLAVFVEQP TPFLPRFLQR LLL LDYPPD RVTLFLHNNE VFHEPHIADS WPQLQDHFSA VKLVGPEEAL SPGEARDMAM DLCRQDPECE FYFSLDADAV LTNL QTLRI LIEENRKVIA PMLSRHGKLW SNFWGALSPD EYYARSEDYV ELVQRKRVGV WNVPYISQAY VIRGDTLRME LPQRD VFSG SDTDPDMAFC KSFRDKGIFL HLSNQHEFGR LLATSRYDTE HLHPDLWQIF DNPVDWKEQY IHENYSRALE GEGIVE QPC PDVYWFPLLS EQMCDELVAE MEHYGQWSGG RHEDSRLAGG YENVPTVDIH MKQVGYEDQW LQLLRTYVGP MTESLFP GY HTKARAVMNF VVRYRPDEQP SLRPHHDSST FTLNVALNHK GLDYEGGGCR FLRYDCVISS PRKGWALLHP GRLTHYHE G LPTTWGTRYI MVSFVDPAAA ENLYFQGDYK DHDGDYKDHD IDYKDDDDKH HHHHHHH

UniProtKB: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

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Macromolecule #2: Procollagen galactosyltransferase 1

MacromoleculeName: Procollagen galactosyltransferase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: procollagen galactosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.976438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFAWSHP QFEKGGGSGG GSGGSAWSHP QFEKSALEVL FQGPGRAAPP GADAYFPEER WSPESPLQAP RVLIALLAR NAAHALPTTL GALERLRHPR ERTALWVATD HNMDNTSTVL REWLVAVKSL YHSVEWRPAE EPRSYPDEEG P KHWSDSRY ...String:
MKTIIALSYI FCLVFAWSHP QFEKGGGSGG GSGGSAWSHP QFEKSALEVL FQGPGRAAPP GADAYFPEER WSPESPLQAP RVLIALLAR NAAHALPTTL GALERLRHPR ERTALWVATD HNMDNTSTVL REWLVAVKSL YHSVEWRPAE EPRSYPDEEG P KHWSDSRY EHVMKLRQAA LKSARDMWAD YILFVDADNL ILNPDTLSLL IAENKTVVAP MLDSRAAYSN FWCGMTSQGY YK RTPAYIP IRKRDRRGCF AVPMVHSTFL IDLRKAASRN LAFYPPHPDY TWSFDDIIVF AFSCKQAEVQ MYVCNKEEYG FLP VPLRAH STLQDEAESF MHVQLEVMVK HPPAEPSRFI SAPTKTPDKM GFDEVFMINL RRRQDRRERM LRALQAQEIE CRLV EAVDG KAMNTSQVEA LGIQMLPGYR DPYHGRPLTK GELGCFLSHY NIWKEVVDRG LQKSLVFEDD LRFEIFFKRR LMNLM RDVE REGLDWDLIY VGRKRMQVEH PEKAVPRVRN LVEADYSYWT LAYVISLQGA RKLLAAEPLS KMLPVDEFLP VMFDKH PVS EYKAHFSLRN LHAFSVEPLL IYPTHYTGDD GYVSDTETSV VWNNEHVKTD WDRAKSQKMR EQQALSREAK NSDVLQS PL DSAARDELAA A

UniProtKB: Procollagen galactosyltransferase 1

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: 2-OXOGLUTARIC ACID

MacromoleculeName: 2-OXOGLUTARIC ACID / type: ligand / ID: 5 / Number of copies: 2 / Formula: AKG
Molecular weightTheoretical: 146.098 Da
Chemical component information

ChemComp-AKG:
2-OXOGLUTARIC ACID

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Macromolecule #6: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #7: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 4 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

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Macromolecule #8: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 8 / Number of copies: 6 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #9: GALACTOSE-URIDINE-5'-DIPHOSPHATE

MacromoleculeName: GALACTOSE-URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: GDU
Molecular weightTheoretical: 566.302 Da
Chemical component information

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 427054
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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