[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleThe structural basis for the human procollagen lysine hydroxylation and dual-glycosylation.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 2436, Year 2025
Publish dateMar 11, 2025
AuthorsJunjiang 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 /
PubMed AbstractThe 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.
External linksNat Commun / PubMed:40069201 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 3.93 Å
Structure data

60075

8zgc

EMDB-60075, PDB-8zgc:
Human lysine O-link glycosylation complex, LH3/ColGalT1 with bound UDP-galactose
Method: EM (single particle) / Resolution: 3.58 Å

60076

8zge

EMDB-60076, PDB-8zge:
Human lysine O-link glycosylation complex, LH3/ColGalT1 tetramer with bound UDP-galactose
Method: EM (single particle) / Resolution: 3.4 Å

60078

8zgg

EMDB-60078, PDB-8zgg:
Human lysine O-link glycosylation complex, LH3/ColGalT1 with bound UDP-glucose
Method: EM (single particle) / Resolution: 3.75 Å

60079

8zgh

EMDB-60079, PDB-8zgh:
Human lysine O-link glycosylation complex, LH3/ColGalT1 in its apo state
Method: EM (single particle) / Resolution: 3.93 Å

Chemicals

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

ChemComp-AKG:
2-OXOGLUTARIC ACID

ChemComp-FE2:
Unknown entry

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

ChemComp-MN:
Unknown entry

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

ChemComp-660:
[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid

Source
  • homo sapiens (human)
KeywordsCYTOSOLIC PROTEIN / complex / hydroxylase / glycosyltransferase / ER protein

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more