8E0P

Crystal structure of mouse APCDD1 in fusion with engineered MBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein.

Hsieh, F.L.Chang, T.H.Gabelli, S.B.Nathans, J.

(2023) Proc Natl Acad Sci U S A 120: e2217096120-e2217096120

  • DOI: https://doi.org/10.1073/pnas.2217096120
  • Primary Citation of Related Structures:  
    8E0P, 8E0R, 8E0W

  • PubMed Abstract: 

    Diverse extracellular proteins negatively regulate WNT signaling. One such regulator is adenomatosis polyposis coli down-regulated 1 (APCDD1), a conserved single-span transmembrane protein. In response to WNT signaling in a variety of tissues, APCDD1 transcripts are highly up-regulated. We have determined the three-dimensional structure of the extracellular domain of APCDD1, and this structure reveals an unusual architecture consisting of two closely apposed β-barrel domains (ABD1 and ABD2). ABD2, but not ABD1, has a large hydrophobic pocket that accommodates a bound lipid. The APCDD1 ECD can also bind to WNT7A, presumably via its covalently bound palmitoleate, a modification that is common to all WNTs and is essential for signaling. This work suggests that APCDD1 functions as a negative feedback regulator by titrating WNT ligands at the surface of responding cells.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein, Protein APCDD1 complex
A, B, C, D
818Escherichia coliMus musculus
This entity is chimeric
Mutation(s): 12 
UniProt & NIH Common Fund Data Resources
Find proteins for C3SHQ8 (Escherichia coli)
Explore C3SHQ8 
Go to UniProtKB:  C3SHQ8
Find proteins for Q3U128 (Mus musculus)
Explore Q3U128 
Go to UniProtKB:  Q3U128
IMPC:  MGI:3513977
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsC3SHQ8Q3U128
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q3U128-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranoseE [auth F],
F [auth G],
G [auth H],
H [auth I]
2N/A
Glycosylation Resources
GlyTouCan:  G66120GK
GlyCosmos:  G66120GK
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMX
Query on DMX

Download Ideal Coordinates CCD File 
FA [auth D],
Y [auth C],
Z [auth C]
3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
C12 H19 N O3 S
MEJASPJNLSQOAG-UHFFFAOYSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
AA [auth C],
L [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
I [auth A]
J [auth A]
BA [auth D],
CA [auth D],
DA [auth D],
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
W [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth D],
M [auth A],
R [auth B],
S [auth B],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth D],
N [auth A],
T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.914α = 90
b = 98.361β = 109.73
c = 156.513γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United States--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary