9U7H | pdb_00009u7h

Complex structure of a glycosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb9U7H/pdb
• EM Map EMD-63936: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2025-03-24 Released: 2026-04-01 
• Deposition Author(s): Yu, H.J., Zhang, M., Sun, H.H., Liu, X.T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Complex structure of a glycosyltransferase

Yu, H.J., Zhang, M., Sun, H.H., Liu, X.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 72.99 kDa 
• Atom Count: 4,454 
• Modeled Residue Count: 538 
• Deposited Residue Count: 622 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Procollagen galactosyltransferase 1	A	613	Homo sapiens	Mutation(s): 0  Gene Names: COLGALT1, GLT25D1, PSEC0241 EC: 2.4.1.50
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBJ5 (Homo sapiens) Explore Q8NBJ5  Go to UniProtKB:  Q8NBJ5
PHAROS:  Q8NBJ5 GTEx:  ENSG00000130309

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-GLY-ALA-LYZ-GLY-GLU-LYS-GLY-SER	B [auth C]	9	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDU (Subject of Investigation/LOI)	C [auth A]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-ABVWGUQPSA-N
UDP (Subject of Investigation/LOI)	E [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MN (Subject of Investigation/LOI)	D [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LYZ	B [auth C]	L-PEPTIDE LINKING	C6 H14 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION
RECONSTRUCTION	RELION
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-04-01 
Deposition Author(s): Yu, H.J., Zhang, M., Sun, H.H., Liu, X.T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-04-01
  Type: Initial release