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- PDB-4yn0: Crystal structure of APP E2 domain in complex with DR6 CRD domain -

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Basic information

Entry
Database: PDB / ID: 4yn0
TitleCrystal structure of APP E2 domain in complex with DR6 CRD domain
Components
  • Amyloid beta A4 protein
  • Tumor necrosis factor receptor superfamily member 21
KeywordsApoptosis/Cell Adhesion / Alzheimer / Neuron pruning / Amyloid precursor protein / Apoptosis-Cell Adhesion complex
Function / homology
Function and homology information


regulation of response to calcium ion / positive regulation of protein import / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of neurotransmitter uptake / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / positive regulation of gene expression, epigenetic / cytosolic mRNA polyadenylation ...regulation of response to calcium ion / positive regulation of protein import / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of neurotransmitter uptake / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / positive regulation of gene expression, epigenetic / cytosolic mRNA polyadenylation / regulation of oligodendrocyte differentiation / endosome to plasma membrane transport vesicle / low-density lipoprotein particle mediated signaling / ECM proteoglycans / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of interleukin-5 production / regulation of dendritic spine maintenance / negative regulation of interleukin-13 production / negative regulation of blood circulation / positive regulation of endothelin production / synaptic assembly at neuromuscular junction / positive regulation of Toll signaling pathway / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / phospholipase D-activating G protein-coupled receptor signaling pathway / positive regulation of G protein-coupled receptor internalization / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / protein trimerization / smooth endoplasmic reticulum calcium ion homeostasis / G alpha (q) signalling events / TAK1-dependent IKK and NF-kappa-B activation / negative regulation of myelination / positive regulation of amyloid precursor protein catabolic process / lipoprotein particle / regulation of amyloid-beta clearance / intermediate-density lipoprotein particle / Platelet degranulation / response to yeast / ciliary rootlet / RAGE receptor binding / G alpha (i) signalling events / antifungal humoral response / regulation of amyloid fibril formation / positive regulation of G protein-coupled receptor signaling pathway / B cell apoptotic process / Mitochondrial protein degradation / low-density lipoprotein particle / COPII-coated ER to Golgi transport vesicle / high-density lipoprotein particle / very-low-density lipoprotein particle / acetylcholine receptor binding / frizzled binding / amyloid-beta complex / growth cone lamellipodium / axonal fasciculation / heparan sulfate proteoglycan binding / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / suckling behavior / microglia development / oligodendrocyte apoptotic process / positive regulation of monocyte chemotaxis / axo-dendritic transport / axon midline choice point recognition / positive regulation of membrane protein ectodomain proteolysis / regulation of synapse structure or activity / hippocampal neuron apoptotic process / astrocyte activation involved in immune response / presynaptic active zone / regulation of spontaneous synaptic transmission / mating behavior / positive regulation of extrinsic apoptotic signaling pathway / growth factor receptor binding / negative regulation of protein localization to nucleus / peptidase activator activity / neuromuscular process controlling balance / PTB domain binding / positive regulation of amyloid fibril formation / Golgi-associated vesicle / negative regulation of interleukin-10 production / regulation of toll-like receptor signaling pathway / astrocyte projection / negative regulation of B cell proliferation / neuron remodeling / negative regulation of neuron differentiation / spindle midzone / chemoattractant activity / nuclear envelope lumen / forebrain development / intracellular vesicle / smooth endoplasmic reticulum / dendrite development / humoral immune response / positive regulation of protein metabolic process / positive regulation of cAMP/PKA signal transduction / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / transition metal ion binding
Similarity search - Function
Tumour necrosis factor receptor 21 / Tumor necrosis factor receptor 21, N-terminal / Tumor necrosis factor receptor 21, death domain / Amyloid precursor protein, E2 domain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. ...Tumour necrosis factor receptor 21 / Tumor necrosis factor receptor 21, N-terminal / Tumor necrosis factor receptor 21, death domain / Amyloid precursor protein, E2 domain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Putative ephrin-receptor like / Death domain profile. / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, heparin-binding / Amyloid A4 N-terminal heparin-binding / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Death-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ribbon / PH-like domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Amyloid-beta precursor protein / Tumor necrosis factor receptor superfamily member 21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsXu, K. / Nikolov, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Genes Dev. / Year: 2015
Title: The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation.
Authors: Xu, K. / Olsen, O. / Tzvetkova-Robev, D. / Tessier-Lavigne, M. / Nikolov, D.B.
History
DepositionMar 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 21
B: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4275
Polymers47,9602
Non-polymers4673
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.320, 67.320, 226.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 21 / Death receptor 6


Mass: 20702.660 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-220
Source method: isolated from a genetically manipulated source
Details: Cysteine rich domain of mouse DR6 protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf21, Dr6 / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q9EPU5
#2: Protein Amyloid beta A4 protein / ABPP / APP / Alzheimer disease amyloid A4 protein homolog / Amyloidogenic glycoprotein / AG


Mass: 27257.801 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 370-592
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: App / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P12023
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 100mM Tris pH 8.6, 18% PEG 8000 / PH range: 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 22, 2014
RadiationMonochromator: Se / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 29375 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.97 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.63
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.34 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.2→40.6 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1421 4.84 %Random selection
Rwork0.2259 ---
obs0.2269 29375 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 29 102 3068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193037
X-RAY DIFFRACTIONf_angle_d1.254082
X-RAY DIFFRACTIONf_dihedral_angle_d16.8591170
X-RAY DIFFRACTIONf_chiral_restr0.056449
X-RAY DIFFRACTIONf_plane_restr0.005542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27630.35341410.3212770X-RAY DIFFRACTION100
2.2763-2.36750.33071480.28892779X-RAY DIFFRACTION100
2.3675-2.47520.32731420.27772808X-RAY DIFFRACTION100
2.4752-2.60570.2811450.2592780X-RAY DIFFRACTION100
2.6057-2.76890.27461680.26462776X-RAY DIFFRACTION100
2.7689-2.98260.33311230.25822803X-RAY DIFFRACTION100
2.9826-3.28270.2931320.25872808X-RAY DIFFRACTION100
3.2827-3.75740.24861370.23812820X-RAY DIFFRACTION100
3.7574-4.73280.21051280.19422807X-RAY DIFFRACTION100
4.7328-40.60130.19481570.18832803X-RAY DIFFRACTION100

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