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- PDB-3u0t: Fab-antibody complex -

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Basic information

Entry
Database: PDB / ID: 3u0t
TitleFab-antibody complex
Components
  • Amyloid beta A4 protein
  • ponezumab HC Fab
  • ponezumab LC Fab
KeywordsIMMUNE SYSTEM / antibody Fab / immunotherapeutic
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / cholesterol metabolic process / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / positive regulation of glycolytic process / extracellular matrix organization / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / Golgi lumen / endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cellular response to amyloid-beta / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation
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. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 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 / PH-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLaPorte, S.L. / Pons, J.P.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Basis of C-terminal beta-Amyloid Peptide Binding by the Antibody Ponezumab for the Treatment of Alzheimer's Disease
Authors: La Porte, S.L. / Bollini, S.S. / Lanz, T.A. / Abdiche, Y.N. / Rusnak, A.S. / Ho, W.H. / Kobayashi, D. / Harrabi, O. / Pappas, D. / Mina, E.W. / Milici, A.J. / Kawabe, T.T. / Bales, K. / Lin, J.C. / Pons, J.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ponezumab LC Fab
D: ponezumab HC Fab
E: Amyloid beta A4 protein
A: ponezumab LC Fab
B: ponezumab HC Fab
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)97,3036
Polymers97,3036
Non-polymers00
Water5,278293
1
C: ponezumab LC Fab
D: ponezumab HC Fab
E: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)48,6523
Polymers48,6523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-38 kcal/mol
Surface area20020 Å2
MethodPISA
2
A: ponezumab LC Fab
B: ponezumab HC Fab
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)48,6523
Polymers48,6523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-37 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.370, 64.250, 95.890
Angle α, β, γ (deg.)90.00, 112.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 214
2111C1 - 214
1121B1 - 212
2121D1 - 212

NCS ensembles :
ID
1
2

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Components

#1: Antibody ponezumab LC Fab


Mass: 24174.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Cells / Production host: Homo sapiens (human)
#2: Antibody ponezumab HC Fab


Mass: 23449.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Cells / Production host: Homo sapiens (human)
#3: Protein/peptide Amyloid beta A4 protein


Mass: 1028.310 Da / Num. of mol.: 2 / Fragment: UNP residues 701-711 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.44→64 Å / Num. all: 35099 / Num. obs: 34993 / % possible obs: 99.7 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.55 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.399 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.752 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26847 1021 3.1 %RANDOM
Rwork0.21858 ---
obs0.22022 31660 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0.01 Å2
2--0.05 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6681 0 0 293 6974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226837
X-RAY DIFFRACTIONr_bond_other_d0.0030.024552
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9639314
X-RAY DIFFRACTIONr_angle_other_deg0.967311153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0285865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09623.916263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.386151100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9421534
X-RAY DIFFRACTIONr_chiral_restr0.0850.21067
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217555
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021327
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_it0.7731.54359
X-RAY DIFFRACTIONr_mcbond_other0.1311.51754
X-RAY DIFFRACTIONr_mcangle_it1.52227079
X-RAY DIFFRACTIONr_scbond_it2.24932478
X-RAY DIFFRACTIONr_scangle_it3.964.52235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2873tight positional0.050.05
22B2586tight positional0.050.05
11A2873tight thermal0.110.5
22B2586tight thermal0.090.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 65 -
Rwork0.286 2337 -
obs--99.67 %
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)
12.3766-0.9874-0.60711.7895-0.10351.75510.0278-0.13510.0591-0.1068-0.0064-0.00390.1034-0.1276-0.02150.0164-0.01330.00250.05220.00930.0281-10.9813-26.925322.5458
21.93130.00461.49060.7218-0.66213.4811-0.0725-0.04040.0986-0.1013-0.01950.0936-0.0106-0.03440.0920.03080.0328-0.01420.0702-0.01190.0752-44.4327-16.29749.278
32.9914-0.18010.5211.92440.09181.82780.19810.20250.0027-0.091-0.1672-0.16240.06680.0894-0.03090.09770.0640.04670.05140.0340.0342-3.3264-22.11340.8056
42.3173-0.51070.530.7345-0.24580.1565-0.0205-0.02910.1811-0.04310.00840.0835-0.01270.00990.01210.08240.00830.02170.08410.02220.0572-28.1707-8.3984.7313
51.2665-0.9238-0.29051.3071-1.23743.77350.1616-0.07230.0591-0.16020.06870.0866-0.061-0.1411-0.23030.06290.0013-0.03570.11170.02020.0824-13.9356.156738.7563
64.3935-0.3557-0.13820.63870.40360.87160.0091-0.0802-0.07890.0628-0.0405-0.11090.00350.00120.03140.01070.0013-0.01490.04280.03020.052518.9578-4.987253.0249
73.3466-0.42330.20020.42890.40931.34660.18160.04360.0632-0.2286-0.07970.03590.00130.1516-0.10190.23220.0788-0.06310.0993-0.03150.0479-2.95862.581618.0456
81.3715-0.62990.69291.257-0.42861.25580.0157-0.0071-0.1305-0.12240.0681-0.03210.13170.0443-0.08390.03580.0050.01570.0352-0.01490.043210.8299-12.287237.6882
93.2359-0.98963.71960.3036-1.14044.2920.78810.8333-0.5085-0.2239-0.19050.17040.79050.9168-0.59760.55610.13870.02650.62950.13670.3354-21.49634.457720.9532
107.02271.3362.05069.8873-0.86770.7688-0.59850.5656-0.1877-0.34340.558-0.7942-0.12860.15030.04040.11470.04740.07870.4168-0.04490.16677.3471-24.521416.1738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 107
2X-RAY DIFFRACTION2A108 - 214
3X-RAY DIFFRACTION3B1 - 82
4X-RAY DIFFRACTION4B83 - 213
5X-RAY DIFFRACTION5C1 - 107
6X-RAY DIFFRACTION6C108 - 214
7X-RAY DIFFRACTION7D1 - 82
8X-RAY DIFFRACTION8D83 - 212
9X-RAY DIFFRACTION9E30 - 40
10X-RAY DIFFRACTION10F30 - 40

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