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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9U7H

This is version 1.0 of the entry. See complete history.

Literature

Complex structure of a glycosyltransferase

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

To be published.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBJ5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
GDU (Subject of Investigation/LOI) Query on GDU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-ABVWGUQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A]	D [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LYZ Query on 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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.