8JL3 | pdb_00008jl3

membrane proteins


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8JL3

This is version 1.3 of the entry. See complete history

Literature

Structure and mechanism of lysosome transmembrane acetylation by HGSNAT.

Xu, R.Ning, Y.Ren, F.Gu, C.Zhu, Z.Pan, X.Pshezhetsky, A.V.Ge, J.Yu, J.

(2024) Nat Struct Mol Biol 31: 1502-1508

  • DOI: https://doi.org/10.1038/s41594-024-01315-5
  • Primary Citation Related Structures: 
    8JKV, 8JL1, 8JL3, 8W4A

  • PubMed Abstract: 

    Lysosomal transmembrane acetylation of heparan sulfates (HS) is catalyzed by HS acetyl-CoA:α-glucosaminide N-acetyltransferase (HGSNAT), whose dysfunction leads to lysosomal storage diseases. The mechanism by which HGSNAT, the sole non-hydrolase enzyme in HS degradation, brings cytosolic acetyl-coenzyme A (Ac-CoA) and lysosomal HS together for N-acyltransferase reactions remains unclear. Here, we present cryogenic-electron microscopy structures of HGSNAT alone, complexed with Ac-CoA and with acetylated products. These structures explain that Ac-CoA binding from the cytosolic side causes dimeric HGSNAT to form a transmembrane tunnel. Within this tunnel, catalytic histidine and asparagine approach the lumen and instigate the transfer of the acetyl group from Ac-CoA to the glucosamine group of HS. Our study unveils a transmembrane acetylation mechanism that may help advance therapeutic strategies targeting lysosomal storage diseases.


  • Organizational Affiliation
    • Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 169.52 kDa 
  • Atom Count: 9,408 
  • Modeled Residue Count: 1,054 
  • Deposited Residue Count: 1,412 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heparan-alpha-glucosaminide N-acetyltransferase
A, B
706Homo sapiensMutation(s): 0 
Gene Names: HGSNATTMEM76
EC: 2.3.1.78
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q68CP4 (Homo sapiens)
Explore Q68CP4 
Go to UniProtKB:  Q68CP4
PHAROS:  Q68CP4
GTEx:  ENSG00000165102 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68CP4
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q68CP4-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
(Subject of Investigation/LOI)

Query on ACO



Download:Ideal Coordinates CCD File
H [auth A],
TA [auth B]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
HB [auth B],
V [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
R16

Query on R16



Download:Ideal Coordinates CCD File
MA [auth A],
YB [auth B]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A],
I [auth A],
SA [auth B],
UA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
C14

Query on C14



Download:Ideal Coordinates CCD File
AB [auth B]
BB [auth B]
CB [auth B]
DB [auth B]
FB [auth B]
AB [auth B],
BB [auth B],
CB [auth B],
DB [auth B],
FB [auth B],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
JB [auth B],
KB [auth B],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
SB [auth B],
T [auth A],
TB [auth B],
UB [auth B],
VB [auth B],
X [auth A],
Y [auth A],
ZA [auth B]
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12

Query on D12



Download:Ideal Coordinates CCD File
BA [auth A]
J [auth A]
NB [auth B]
QA [auth A]
RA [auth B]
BA [auth A],
J [auth A],
NB [auth B],
QA [auth A],
RA [auth B],
VA [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10

Query on D10



Download:Ideal Coordinates CCD File
AA [auth A],
MB [auth B]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT

Query on OCT



Download:Ideal Coordinates CCD File
AC [auth B]
BC [auth B]
CA [auth A]
DA [auth A]
EA [auth A]
AC [auth B],
BC [auth B],
CA [auth A],
DA [auth A],
EA [auth A],
EB [auth B],
FA [auth A],
GB [auth B],
IB [auth B],
K [auth A],
KA [auth A],
L [auth A],
LA [auth A],
LB [auth B],
M [auth A],
NA [auth A],
OA [auth A],
OB [auth B],
PA [auth A],
PB [auth B],
QB [auth B],
RB [auth B],
S [auth A],
U [auth A],
W [auth A],
WA [auth B],
WB [auth B],
XA [auth B],
XB [auth B],
YA [auth B],
Z [auth A],
ZB [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2025-06-18
    Changes: Data collection