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- PDB-3bae: Crystal structure of Fab WO2 bound to the N terminal domain of Am... -

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Basic information

Entry
Database: PDB / ID: 3bae
TitleCrystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
Components
  • Amyloid Beta Peptide
  • WO2 IgG2a Fab fragment Heavy Chain
  • WO2 IgG2a Fab fragment Light Chain Kappa
KeywordsIMMUNE SYSTEM / Abeta / amyloid beta peptide / Fab / WO2 / alzheimer's disease / immunotherapies / APP
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 / immunoglobulin complex / positive regulation of amyloid fibril formation / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / transition metal ion binding / main axon / regulation of multicellular organism growth / intracellular copper ion homeostasis / 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 mitotic cell cycle / axonogenesis / positive regulation of calcium-mediated signaling / response to interleukin-1 / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / positive regulation of interleukin-1 beta production / adult locomotory behavior / endosome lumen / dendritic shaft / positive regulation of long-term synaptic potentiation / trans-Golgi network membrane / TAK1-dependent IKK and NF-kappa-B activation / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / positive regulation of non-canonical NF-kappaB signal transduction / regulation of long-term neuronal synaptic plasticity / synapse organization / cellular response to nerve growth factor stimulus / recycling endosome / visual learning / positive regulation of interleukin-6 production / response to lead ion / Golgi lumen / cognition / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / cellular response to amyloid-beta / neuron projection development / 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
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, 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / Amyloid-beta precursor protein / Anti-human Fc gamma receptor III 3G8 gamma heavy chain variable region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.593 Å
AuthorsMiles, L.A. / Wun, K.S. / Crespi, G.A. / Parker, M.W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.
Authors: Miles, L.A. / Wun, K.S. / Crespi, G.A. / Fodero-Tavoletti, M.T. / Galatis, D. / Bagley, C.J. / Beyreuther, K. / Masters, C.L. / Cappai, R. / McKinstry, W.J. / Barnham, K.J. / Parker, M.W.
History
DepositionNov 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 1.3Nov 20, 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
L: WO2 IgG2a Fab fragment Light Chain Kappa
H: WO2 IgG2a Fab fragment Heavy Chain
A: Amyloid Beta Peptide


Theoretical massNumber of molelcules
Total (without water)52,2463
Polymers52,2463
Non-polymers00
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-25.6 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.658, 66.365, 115.337
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: Antibody WO2 IgG2a Fab fragment Light Chain Kappa


Mass: 24139.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS
#2: Antibody WO2 IgG2a Fab fragment Heavy Chain


Mass: 24837.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q811U5*PLUS
#3: Protein/peptide Amyloid Beta Peptide


Mass: 3268.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: A-beta 1-28 was prepared synthetically / References: UniProt: P05067*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 1.81 Å3/Da / Density % sol: 31.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM bicine, 200mM MgCl2, 20% w/v PEG 8000 , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: cappilary optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→20.383 Å / Num. all: 53416 / Num. obs: 53254 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.49 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.4
Reflection shellResolution: 1.593→1.634 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3785 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PLG

1plg


Resolution: 1.593→20.38 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.425 / SU ML: 0.085 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24968 2681 5 %RANDOM
Rwork0.2068 ---
obs0.20897 50573 99.7 %-
all-53416 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.853 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.593→20.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 0 466 3909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223530
X-RAY DIFFRACTIONr_bond_other_d0.0020.022374
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9514796
X-RAY DIFFRACTIONr_angle_other_deg0.93135791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22723.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39215572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7041520
X-RAY DIFFRACTIONr_chiral_restr0.0970.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02720
X-RAY DIFFRACTIONr_nbd_refined0.1880.2607
X-RAY DIFFRACTIONr_nbd_other0.2090.22436
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21660
X-RAY DIFFRACTIONr_nbtor_other0.0850.21889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3260.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0681.52820
X-RAY DIFFRACTIONr_mcbond_other0.2331.5890
X-RAY DIFFRACTIONr_mcangle_it1.29223597
X-RAY DIFFRACTIONr_scbond_it2.24131574
X-RAY DIFFRACTIONr_scangle_it2.9444.51199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.593→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 184 -
Rwork0.291 3601 -
all-3785 -
obs-3785 100 %

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