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- PDB-3bkj: Crystal structure of Fab wo2 bound to the n terminal domain of am... -

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Basic information

Entry
Database: PDB / ID: 3bkj
TitleCrystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
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 / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway ...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 / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / 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 / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / 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 / positive regulation of protein metabolic process / dendrite development / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / immunoglobulin mediated immune response / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / main axon / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / ECM proteoglycans / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / antigen binding / positive regulation of chemokine production / cellular response to manganese ion / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / adult locomotory behavior / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / dendritic shaft / 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 / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / cellular response to nerve growth factor stimulus / visual learning / recycling endosome / response to lead ion / positive regulation of interleukin-6 production / 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 gene expression / regulation of translation / early endosome membrane / G alpha (i) 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Ig heavy chain Mem5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsMiles, L.A. / Wun, K.S. / Crespi, G.A. / Fodero-Tavoletti, M. / Galatis, D. / Bageley, C.J. / Beyreuther, K. / Masters, C.L. / Cappai, R. / McKinstry, W.J. ...Miles, L.A. / Wun, K.S. / Crespi, G.A. / Fodero-Tavoletti, M. / Galatis, D. / Bageley, C.J. / Beyreuther, K. / Masters, C.L. / Cappai, R. / McKinstry, W.J. / Barnham, K.J. / 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
DepositionDec 6, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
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)54,2113
Polymers54,2113
Non-polymers00
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-27 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.743, 66.632, 115.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody WO2 IgG2a Fab fragment Light Chain Kappa


Mass: 27817.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: balb/c / References: UniProt: A2NHM3*PLUS
#2: Antibody WO2 IgG2a Fab fragment Heavy Chain


Mass: 24433.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: balb/c / References: UniProt: P84751*PLUS
#3: Protein/peptide Amyloid Beta Peptide


Mass: 1960.047 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Amyloid beta peptide residues 1-16 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: 1.83 Å3/Da / Density % sol: 32.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 25% (v/v) PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2003
Details: bent conical Si-mirror (Rh coating); bent cylindrical Ge(111) monochromator
RadiationMonochromator: bent cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→20.12 Å / Num. all: 53898 / Num. obs: 53462 / % possible obs: 99.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.3
Reflection shellResolution: 1.593→1.634 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3514 / % possible all: 92.23

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→20.12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.973 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.108 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5263 9.8 %RANDOM
Rwork0.188 ---
all0.21 53462 --
obs0.192 53462 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.355 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 0 466 3941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223563
X-RAY DIFFRACTIONr_bond_other_d0.0020.022399
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9514851
X-RAY DIFFRACTIONr_angle_other_deg0.8853.0035843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9823.427143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52915576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5531520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_nbd_refined0.1890.2543
X-RAY DIFFRACTIONr_nbd_other0.2090.22432
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21695
X-RAY DIFFRACTIONr_nbtor_other0.0840.21962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2306
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.239
X-RAY DIFFRACTIONr_mcbond_it1.1591.52847
X-RAY DIFFRACTIONr_mcbond_other0.2181.5901
X-RAY DIFFRACTIONr_mcangle_it1.41623639
X-RAY DIFFRACTIONr_scbond_it2.40531583
X-RAY DIFFRACTIONr_scangle_it3.0944.51212
LS refinement shellResolution: 1.593→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 348 -
Rwork0.24 3166 -
all-3514 -
obs-3514 92.23 %

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