6YXH

Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 A resolution determined by Serial Crystallography (SSX) using CrystalDirect


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An automated platform for structural analysis of membrane proteins through serial crystallography.

Healey, R.D.Basu, S.Humm, A.S.Leyrat, C.Cong, X.Golebiowski, J.Dupeux, F.Pica, A.Granier, S.Marquez, J.A.

(2021) Cell Rep Methods 1: None-None

  • DOI: https://doi.org/10.1016/j.crmeth.2021.100102
  • Primary Citation of Related Structures:  
    6YX9, 6YXD, 6YXF, 6YXG, 6YXH

  • PubMed Abstract: 

    Membrane proteins are central to many pathophysiological processes, yet remain very difficult to analyze structurally. Moreover, high-throughput structure-based drug discovery has not yet been exploited for membrane proteins because of lack of automation. Here, we present a facile and versatile platform for in meso membrane protein crystallization, enabling rapid atomic structure determination at both cryogenic and room temperatures. We apply this approach to human integral membrane proteins, which allowed us to identify different conformational states of intramembrane enzyme-product complexes and analyze by molecular dynamics simulations the structural dynamics of the ADIPOR2 integral membrane protein. Finally, we demonstrate an automated pipeline combining high-throughput microcrystal soaking, automated laser-based harvesting, and serial crystallography, enabling screening of small-molecule libraries with membrane protein crystals grown in meso . This approach brings needed automation to this important class of drug targets and enables high-throughput structure-based ligand discovery with membrane proteins.


  • Organizational Affiliation

    IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkaline ceramidase 3350Homo sapiensMutation(s): 0 
Gene Names: ACER3APHCPHCA
EC: 3.5.1 (PDB Primary Data), 3.5.1.23 (PDB Primary Data)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUN7 (Homo sapiens)
Explore Q9NUN7 
Go to UniProtKB:  Q9NUN7
PHAROS:  Q9NUN7
GTEx:  ENSG00000078124 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NUN7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
K [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.47α = 90
b = 69.97β = 90
c = 259.49γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union647687
European CommissionEuropean Union653706
European CommissionEuropean Union871037

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Advisory, Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description