8E0P | pdb_00008e0p

Crystal structure of mouse APCDD1 in fusion with engineered MBP

PDB DOI: https://doi.org/10.2210/pdb8E0P/pdb

Classification: SIGNALING PROTEIN
Organism(s): Escherichia coli, Mus musculus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-08-09 Released: 2023-05-03
Deposition Author(s): Hsieh, F.L., Chang, T.H., Gabelli, S.B., Nathans, J.
Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.239 (Depositor), 0.238 (DCC)
R-Value Work:
0.192 (Depositor), 0.206 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 37155902 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2217096120
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 372.51 kDa
Atom Count: 25,921
Modeled Residue Count: 3,133
Deposited Residue Count: 3,272
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein, Protein APCDD1 complex	A, B, C, D	818	Escherichia coli, Mus 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	C3SHQ8 Q3U128
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q3U128-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	E [auth F], F [auth G], G [auth H], H [auth I]	2		N/A	Interactions Focus chain E [auth F] Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I] Interactions & Density Focus chain E [auth F] Focus chain F [auth G] Focus chain G [auth H] Focus chain H [auth I]
Glycosylation Resources
GlyTouCan: G66120GK GlyCosmos: G66120GK

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMX Query on DMX Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	FA [auth D], Y [auth C], Z [auth C]	3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE C₁₂ H₁₉ N O₃ S MEJASPJNLSQOAG-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain Y [auth C] Focus chain Z [auth C]
PLM (Subject of Investigation/LOI) Query on PLM Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain L [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain L [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain L [auth A]	AA [auth C], L [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain L [auth A] Interactions & Density Focus chain AA [auth C] Focus chain L [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C]	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		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C]	EA [auth D], M [auth A], R [auth B], S [auth B], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain N [auth A] SDF format, chain T [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B]	GA [auth D], N [auth A], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth D] Focus chain N [auth A] Focus chain T [auth B] Interactions & Density Focus chain GA [auth D] Focus chain N [auth A] Focus chain T [auth B]