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- PDB-4hix: Crystal structure of a humanised 3D6 Fab bound to amyloid beta peptide -

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Basic information

Entry
Database: PDB / ID: 4hix
TitleCrystal structure of a humanised 3D6 Fab bound to amyloid beta peptide
Components
  • Beta-amyloid protein 40
  • Humanized 3D6 Fab heavy chain
  • Humanized 3D6 Fab light chain
KeywordsPROTEIN FIBRIL/Immune System / immunoglobulin / immunotherapy candidate / amyloid beta peptide / PROTEIN FIBRIL-Immune System complex
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / complement-dependent cytotoxicity / CD22 mediated BCR regulation / antibody-dependent cellular cytotoxicity / amyloid-beta complex / growth cone lamellipodium / Aggregated β-amyloid induces FXII autocatalysis ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / complement-dependent cytotoxicity / CD22 mediated BCR regulation / antibody-dependent cellular cytotoxicity / amyloid-beta complex / growth cone lamellipodium / Aggregated β-amyloid induces FXII autocatalysis / Fc epsilon receptor (FCERI) signaling / cellular response to norepinephrine stimulus / Fc-gamma receptor I complex binding / collateral sprouting in absence of injury / growth cone filopodium / hippocampal neuron apoptotic process / microglia development / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / Aggregated β-amyloid interacts with fibrinogen / axon midline choice point recognition / regulation of synapse structure or activity / positive regulation of synaptic transmission, cholinergic / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / immunoglobulin complex, circulating / regulation of spontaneous synaptic transmission / mating behavior / Classical antibody-mediated complement activation / growth factor receptor binding / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / complement activation, classical pathway / peptidase activator activity / PTB domain binding / Golgi-associated vesicle / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / neuron remodeling / astrocyte projection / regulation of multicellular organism growth / nuclear envelope lumen / dendrite development / TRAF6 mediated NF-kB activation / FCGR activation / positive regulation of protein metabolic process / negative regulation of long-term synaptic potentiation / signaling receptor activator activity / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / Role of LAT2/NTAL/LAB on calcium mobilization / intracellular copper ion homeostasis / modulation of excitatory postsynaptic potential / main axon / ECM proteoglycans / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / positive regulation of T cell migration / response to insulin-like growth factor stimulus / regulation of presynapse assembly / extracellular matrix organization / swimming behavior / adult locomotory behavior / regulation of long-term neuronal synaptic plasticity / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / positive regulation of chemokine production / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / cellular response to cAMP / neuron projection maintenance / clathrin-coated pit / FCERI mediated Ca+2 mobilization / visual learning / astrocyte activation / B cell receptor signaling pathway / synaptic cleft / FCGR3A-mediated IL10 synthesis / Mitochondrial protein degradation / platelet alpha granule lumen / regulation of neuron apoptotic process / positive regulation of glycolytic process / response to interleukin-1 / Regulation of Complement cascade / ionotropic glutamate receptor signaling pathway / locomotory behavior / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cellular response to copper ion / learning / endosome lumen / Cell surface interactions at the vascular wall / positive regulation of interleukin-1 beta production
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, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...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 / 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, 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 / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / PH-like domain superfamily / 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
Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1 / Amyloid-beta precursor protein
Similarity search - Component
Biological specieshomo Sapiens (human)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.204 Å
AuthorsMiles, L.A. / Crespi, G.A.N. / Parker, M.W.
CitationJournal: Sci Rep / Year: 2013
Title: Bapineuzumab captures the N-terminus of the Alzheimer's disease amyloid-beta peptide in a helical conformation.
Authors: Miles, L.A. / Crespi, G.A. / Doughty, L. / Parker, M.W.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Structure summary
Revision 1.2Oct 2, 2013Group: Source and taxonomy
Revision 1.3Mar 19, 2014Group: Source and taxonomy
Revision 1.4Nov 20, 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
H: Humanized 3D6 Fab heavy chain
L: Humanized 3D6 Fab light chain
A: Beta-amyloid protein 40


Theoretical massNumber of molelcules
Total (without water)51,6953
Polymers51,6953
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-22 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.343, 83.039, 91.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11H-376-

HOH

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Components

#1: Antibody Humanized 3D6 Fab heavy chain


Mass: 24264.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo Sapiens, Mus musculus / References: UniProt: P01857*PLUS
#2: Antibody Humanized 3D6 Fab light chain


Mass: 24161.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo Sapiens, Mus musculus / References: UniProt: P01834*PLUS
#3: Protein/peptide Beta-amyloid protein 40 / Beta-APP40


Mass: 3268.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: sodium formate, PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2012
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionRedundancy: 12.1 % / Av σ(I) over netI: 13.68 / Number: 280015 / Rmerge(I) obs: 0.163 / Χ2: 1 / D res high: 2.2 Å / D res low: 100 Å / Num. obs: 23109 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.7410099.810.0910.97813.4
3.764.7410010.1020.96414.2
3.293.7610010.1250.9914.4
2.993.2910010.1710.97714.5
2.772.9910010.2430.93314.5
2.612.7710010.3591.05414.6
2.482.6110010.4740.99712.9
2.372.4810010.5551.0548.9
2.282.3797.910.6160.9156.9
2.22.2889.810.7881.2215.8
ReflectionResolution: 2.2→100 Å / Num. all: 23109 / Num. obs: 23109 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.1 % / Rmerge(I) obs: 0.163 / Χ2: 0.995 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.285.80.78820601.221189.8
2.28-2.376.90.61622580.915197.9
2.37-2.488.90.55522881.0541100
2.48-2.6112.90.47422960.9971100
2.61-2.7714.60.35923071.0541100
2.77-2.9914.50.24323250.9331100
2.99-3.2914.50.17123410.9771100
3.29-3.7614.40.12523460.991100
3.76-4.7414.20.10223770.9641100
4.74-10013.40.09125110.978199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å49.74 Å
Translation2.2 Å49.74 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.204→48.281 Å / Occupancy max: 1 / Occupancy min: 0.76 / FOM work R set: 0.8584 / SU ML: 0.21 / σ(F): 0.07 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 2000 9.05 %random
Rwork0.1695 ---
obs0.1741 22096 94.37 %-
all-22096 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.96 Å2 / Biso mean: 20.779 Å2 / Biso min: 4.07 Å2
Refinement stepCycle: LAST / Resolution: 2.204→48.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 0 237 3615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053460
X-RAY DIFFRACTIONf_angle_d0.9814693
X-RAY DIFFRACTIONf_chiral_restr0.065522
X-RAY DIFFRACTIONf_plane_restr0.004602
X-RAY DIFFRACTIONf_dihedral_angle_d12.8221244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.204-2.25880.31251080.22991080118874
2.2588-2.31990.26221260.21291273139985
2.3199-2.38810.31581330.20221332146590
2.3881-2.46520.27421390.19681406154593
2.4652-2.55330.26141400.1791397153794
2.5533-2.65550.27261420.18021426156896
2.6555-2.77640.23371460.18151467161397
2.7764-2.92280.24251470.16981470161797
2.9228-3.10580.2511490.17471500164998
3.1058-3.34560.21191480.16541493164199
3.3456-3.68220.1941510.15291517166899
3.6822-4.21470.18861510.14661525167699
4.2147-5.3090.1651560.132715621718100
5.309-48.2810.20291640.192716481812100

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