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- PDB-8s4y: Crystal structure of an APP-talin (F2F3) chimera -

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Basic information

Entry
Database: PDB / ID: 8s4y
TitleCrystal structure of an APP-talin (F2F3) chimera
Components
  • C31
  • Talin-1
KeywordsCELL ADHESION / Amyloid precursor protein / talin / FERM domains / chimera / Alzheimer's disease
Function / homology
Function and homology information


Formyl peptide receptors bind formyl peptides and many other ligands / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / cytosolic mRNA polyadenylation / ECM proteoglycans / synaptic assembly at neuromuscular junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...Formyl peptide receptors bind formyl peptides and many other ligands / negative regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / cytosolic mRNA polyadenylation / ECM proteoglycans / synaptic assembly at neuromuscular junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / smooth endoplasmic reticulum calcium ion homeostasis / TAK1-dependent IKK and NF-kappa-B activation / G alpha (q) signalling events / G alpha (i) signalling events / Platelet degranulation / ciliary rootlet / Mitochondrial protein degradation / COPII-coated ER to Golgi transport vesicle / suckling behavior / collateral sprouting in absence of injury / axo-dendritic transport / regulation of synapse structure or activity / axon midline choice point recognition / central nervous system neuron differentiation / presynaptic active zone / mating behavior / Golgi-associated vesicle / neuromuscular process controlling balance / neuron remodeling / negative regulation of neuron differentiation / spindle midzone / intracellular vesicle / forebrain development / dendrite development / smooth endoplasmic reticulum / signaling receptor activator activity / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / positive regulation of G2/M transition of mitotic cell cycle / cholesterol metabolic process / ruffle / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / axonogenesis / adult locomotory behavior / locomotory behavior / neuromuscular junction / serine-type endopeptidase inhibitor activity / cell-cell adhesion / neuron cellular homeostasis / recycling endosome / visual learning / structural constituent of cytoskeleton / G2/M transition of mitotic cell cycle / ruffle membrane / cognition / memory / integrin binding / long-term synaptic potentiation / endocytosis / neuron differentiation / neuron projection development / apical part of cell / actin filament binding / synaptic vesicle / cell-cell junction / mitotic cell cycle / heparin binding / regulation of translation / growth cone / regulation of gene expression / response to oxidative stress / cytoplasmic vesicle / neuron apoptotic process / perikaryon / gene expression / cytoskeleton / early endosome / receptor complex / cell adhesion / neuron projection / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / axon / focal adhesion / protein kinase binding / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / nucleus / membrane
Similarity search - Function
Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain ...Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / 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. / 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, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / FERM central domain / FERM/acyl-CoA-binding protein superfamily / 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 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBall, N.J. / Ellis, C. / Goult, B.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Open Biology / Year: 2024
Title: The structure of an amyloid precursor protein/talin complex indicates a mechanical basis of Alzheimer's disease.
Authors: Ellis, C. / Ward, N.L. / Rice, M. / Ball, N.J. / Walle, P. / Najdek, C. / Kilinc, D. / Lambert, J.C. / Chapuis, J. / Goult, B.T.
History
DepositionFeb 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C31
B: Talin-1


Theoretical massNumber of molelcules
Total (without water)24,1432
Polymers24,1432
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-4 kcal/mol
Surface area12920 Å2
Unit cell
Length a, b, c (Å)60.388, 64.081, 65.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide C31


Mass: 1992.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residual vector sequence after TEV cleavage (GIDPFT); Amyloid Precursor Protein (Q754-F764)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: App, A4, AD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12023
#2: Protein Talin-1


Mass: 22150.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mTalin1 F2F3 (residues 209-400) / Source: (gene. exp.) Mus musculus (house mouse) / Gene: TLN1, TLN / Production host: Escherichia coli (E. coli) / References: UniProt: P54939
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 10% v/v ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95375 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 2.7→45.7 Å / Num. obs: 7374 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 49.74 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.128 / Net I/σ(I): 12.8
Reflection shellResolution: 2.7→2.74 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 359 / CC1/2: 0.832 / Rpim(I) all: 0.33 / Rrim(I) all: 0.85 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.7 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 729 9.96 %
Rwork0.2109 --
obs0.2167 7322 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 0 8 1678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.032
X-RAY DIFFRACTIONf_dihedral_angle_d6.453233
X-RAY DIFFRACTIONf_chiral_restr0.056247
X-RAY DIFFRACTIONf_plane_restr0.012309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.36151430.27811269X-RAY DIFFRACTION99
2.91-3.20.36761510.25521289X-RAY DIFFRACTION99
3.2-3.660.27491400.24181300X-RAY DIFFRACTION100
3.66-4.610.23341410.1841341X-RAY DIFFRACTION100
4.61-45.70.23981540.19161394X-RAY DIFFRACTION100

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