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- PDB-3moq: Amyloid beta(18-41) peptide fusion with new antigen receptor vari... -

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Basic information

Entry
Database: PDB / ID: 3moq
TitleAmyloid beta(18-41) peptide fusion with new antigen receptor variable domain from sharks
ComponentsNew antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain
KeywordsNEUROPEPTIDE / IMMUNE SYSTEM / AB-IGNAR / AB-12Y-2 / RECEPTOR / AMYLOID / GLYCOPROTEIN / MEMBRANE / PROTEASE INHIBITOR / SERINE PROTEASE INHIBITOR / TRANSMEMBRANE / AMYLOID BETA FUSION WITH IGNAR / CHIMERA OF IMMUNE SYSTEM AND AMYLOID PEPTIDE
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / main axon / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / protein serine/threonine kinase binding / response to interleukin-1 / platelet alpha granule lumen / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / endosome lumen / positive regulation of interleukin-1 beta production / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / adult locomotory behavior / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / recycling endosome / synapse organization / visual learning / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / neuron projection development / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression / early endosome membrane / G alpha (i) signalling events / perikaryon / G alpha (q) signalling events / dendritic spine
Similarity search - Function
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, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...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, amyloid-beta peptide superfamily / 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 / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein / New antigen receptor variable domain
Similarity search - Component
Biological speciesOrectolobus maculatus (spotted wobbegong)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsStreltsov, V.A.
CitationJournal: J.Neurosci. / Year: 2011
Title: Crystal Structure of the Amyloid-{beta} p3 Fragment Provides a Model for Oligomer Formation in Alzheimer's Disease
Authors: Streltsov, V.A. / Varghese, J.N. / Masters, C.L. / Nuttall, S.D.
History
DepositionApr 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain
B: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain
C: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain
D: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)53,8654
Polymers53,8654
Non-polymers00
Water10,070559
1
A: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)13,4661
Polymers13,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)13,4661
Polymers13,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)13,4661
Polymers13,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain


Theoretical massNumber of molelcules
Total (without water)13,4661
Polymers13,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-32 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.653, 79.653, 85.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
New antigen receptor variable domain,P3(40) peptide from Amyloid beta A4 protein,New antigen receptor variable domain / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 13466.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF NEW ANTIGEN RECEPTOR VARIABLE DOMAIN (RESIDUES 1-87 AND 102-113 FROM UNP Q6X1E6) INSERTED WITH AMYLOID BETA 18-41 (RESIDUES 689-712 FROM UNP P05067)
Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong), (gene. exp.) Homo sapiens (human)
Plasmid: PGC / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6X1E6, UniProt: P05067
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 6000, 0.2M AMMONIUM CHLORIDE, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95664 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95664 Å / Relative weight: 1
ReflectionResolution: 2.054→26.329 Å / Num. obs: 35851 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.09
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VER

1ver


Resolution: 2.054→26.07 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.305 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24892 1914 5.1 %RANDOM
Rwork0.18991 ---
obs0.19291 35851 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.834 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å20 Å2
2---0.8 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.054→26.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 0 559 4339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.955172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2515500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32723.947152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31115664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5451524
X-RAY DIFFRACTIONr_chiral_restr0.1110.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.52456
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08823920
X-RAY DIFFRACTIONr_scbond_it1.6531380
X-RAY DIFFRACTIONr_scangle_it2.74.51252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.054→2.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 151 -
Rwork0.236 2597 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.08431.0793-2.15721.248-1.28754.2376-0.1366-0.0393-0.1188-0.30840.0249-0.24480.32590.13680.11170.21650.04640.06140.1550.03330.07764.1790.902-21.476
24.16481.32342.23390.65130.37382.11060.0518-0.4079-0.13690.0323-0.096-0.0988-0.1092-0.18050.04420.23910.0207-0.0420.1972-0.05580.092422.148-14.733-12.076
31.5804-0.9134-1.90861.07091.10462.4168-0.0180.0133-0.01080.0527-0.00810.09420.03280.00370.02610.11770.0029-0.01690.1509-0.00760.021935.7627.5435.987
42.2371-4.46724.320812.633-9.965811.8740.74740.66190.0859-1.77-1.4109-0.71251.61371.74110.66350.43650.22170.12770.45550.13580.19260.028-29.057-3.911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 126
2X-RAY DIFFRACTION2B1 - 126
3X-RAY DIFFRACTION3C1 - 126
4X-RAY DIFFRACTION4D1 - 126

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