4YN0 | pdb_00004yn0

Crystal structure of APP E2 domain in complex with DR6 CRD domain

PDB DOI: https://doi.org/10.2210/pdb4YN0/pdb

Classification: Apoptosis/Cell Adhesion
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-03-08 Released: 2015-04-15
Deposition Author(s): Xu, K., Nikolov, D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.245 (Depositor), 0.246 (DCC)
R-Value Work:
0.226 (Depositor), 0.230 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation.

Xu, K., Olsen, O., Tzvetkova-Robev, D., Tessier-Lavigne, M., Nikolov, D.B.

(2015) Genes Dev 29: 785-790

PubMed: 25838500 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/gad.257675.114
Primary Citation Related Structures:
4YN0

PubMed Abstract:
The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.

Organizational Affiliation

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA;

Macromolecule Content

Total Structure Weight: 48.43 kDa
Atom Count: 3,068
Modeled Residue Count: 370
Deposited Residue Count: 423
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 21	A	190	Mus musculus	Mutation(s): 0 Gene Names: Tnfrsf21, Dr6
UniProt
Find proteins for Q9EPU5 (Mus musculus) Explore Q9EPU5 Go to UniProtKB: Q9EPU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9EPU5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q9EPU5-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	B	233	Mus musculus	Mutation(s): 0 Gene Names: App
UniProt & NIH Common Fund Data Resources
Find proteins for P12023 (Mus musculus) Explore P12023 Go to UniProtKB: P12023
IMPC: MGI:88059
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12023
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: P12023-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.245 (Depositor), 0.246 (DCC)
R-Value Work: 0.226 (Depositor), 0.230 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.32	α = 90
b = 67.32	β = 90
c = 226.229	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Xu, K.

Nikolov, D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103403
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2015-04-29
Changes: Database references
Version 1.2: 2017-09-20
Changes: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
Version 1.3: 2019-12-04
Changes: Author supporting evidence
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2024-10-30
Changes: Data collection, Database references, Structure summary