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- PDB-4onf: Fab fragment of 3D6 in complex with amyloid beta 1-7 -

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Basic information

Entry
Database: PDB / ID: 4onf
TitleFab fragment of 3D6 in complex with amyloid beta 1-7
Components
  • 3D6 FAB ANTIBODY HEAVY CHAIN
  • 3D6 FAB ANTIBODY LIGHT CHAIN
  • Amyloid beta A4 protein
KeywordsIMMUNE SYSTEM / ANTIBODY / AMYLOID BETA PEPTIDE
Function / homology
Function and homology information


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / positive regulation of protein metabolic process / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / response to interleukin-1 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / cell-cell junction / Platelet degranulation
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 / PH-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFeinberg, H. / Saldanha, J.W. / Diep, L. / Goel, A. / Widom, A. / Veldman, G.M. / Weis, W.I. / Schenk, D. / Basi, G.S.
CitationJournal: Alzheimers Res Ther / Year: 2014
Title: Crystal structure reveals conservation of amyloid-beta conformation recognized by 3D6 following humanization to bapineuzumab.
Authors: Feinberg, H. / Saldanha, J.W. / Diep, L. / Goel, A. / Widom, A. / Veldman, G.M. / Weis, W.I. / Schenk, D. / Basi, G.S.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 3D6 FAB ANTIBODY HEAVY CHAIN
L: 3D6 FAB ANTIBODY LIGHT CHAIN
P: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)48,9823
Polymers48,9823
Non-polymers00
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-22 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.81, 69.44, 61.73
Angle α, β, γ (deg.)90.0, 115.43, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 3D6 FAB ANTIBODY HEAVY CHAIN


Mass: 23827.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 3D6 FAB ANTIBODY LIGHT CHAIN


Mass: 24263.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Amyloid beta A4 protein


Mass: 890.897 Da / Num. of mol.: 1 / Fragment: unp residues 672-678 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% Peg400, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→59.376 Å / Num. obs: 32824 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22.99 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.70.233.2898524050.23100
2.05-2.113.70.1983.6880123470.198100
2.11-2.173.80.1724.2865923050.172100
2.17-2.243.80.1464.9825821990.146100
2.24-2.313.70.1325.3816321770.132100
2.31-2.393.80.1245.8786820930.124100
2.39-2.483.80.1116.3761420180.111100
2.48-2.583.80.0977735519510.097100
2.58-2.73.80.097.6689218280.0999.9
2.7-2.833.80.0778.6671217830.077100
2.83-2.983.80.06410.1639216990.064100
2.98-3.163.80.05711.3609916160.057100
3.16-3.383.80.05111.4562514940.051100
3.38-3.653.80.05111.1532814170.051100
3.65-43.80.05111.3491813050.051100
4-4.473.80.04611.9444811780.046100
4.47-5.163.80.04711.6393810460.047100
5.16-6.323.70.04710.332608730.047100
6.32-8.943.70.03815.325916990.038100
8.94-59.3763.50.04213.313603910.04299.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-IceIcedata collection
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IFL

3ifl


Resolution: 2→35.097 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8761 / SU ML: 0.18 / σ(F): 0 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 1664 5.07 %
Rwork0.1576 --
obs0.1599 32814 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.58 Å2 / Biso mean: 28.5434 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: LAST / Resolution: 2→35.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 390 3748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073476
X-RAY DIFFRACTIONf_angle_d1.0954728
X-RAY DIFFRACTIONf_chiral_restr0.085532
X-RAY DIFFRACTIONf_plane_restr0.004597
X-RAY DIFFRACTIONf_dihedral_angle_d12.2221254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0001-2.05890.24381330.1726082741
2.0589-2.12530.22811210.165525822703
2.1253-2.20130.21881380.165925722710
2.2013-2.28940.25331420.168325752717
2.2894-2.39360.22551320.164126002732
2.3936-2.51980.22521370.165425772714
2.5198-2.67760.21371530.168525872740
2.6776-2.88420.21971200.172925982718
2.8842-3.17430.21191520.172725812733
3.1743-3.63320.21031520.160225962748
3.6332-4.57590.17321170.133826242741
4.5759-35.10260.16631670.145126502817
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)
13.5534-1.61090.07922.3795-0.30231.7918-0.0463-0.01990.05420.0411-0.0235-0.0205-0.0674-0.080.06530.13190.00280.00050.1063-0.00380.100215.36585.416237.6387
22.10550.6943-0.88341.7993-1.18825.7052-0.0490.22550.1432-0.16370.0068-0.0628-0.48460.20160.02230.2215-0.02920.0030.28310.01090.145943.32375.584518.9862
32.4385-0.0677-0.75691.9701-0.9223.29190.00440.04-0.0937-0.1544-0.04070.00540.1337-0.00980.03440.10170.0031-0.01050.1147-0.02020.12145.29846.989618.6093
43.6144-1.77812.04452.468-1.87243.60850.0142-0.0424-0.1809-0.00180.0313-0.00290.09580.0845-0.05090.1586-0.01010.02960.2048-0.00010.147538.8142-4.2356.2345
58.6001-3.4095-0.37252.58683.50839.2122-0.3812-0.37640.0610.25660.2660.5604-0.0446-1.04570.13140.17590.03710.01510.2360.02690.16820.08665.911536.9598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 119 )H0
2X-RAY DIFFRACTION2chain 'H' and (resid 120 through 219 )H0
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 111 )L0
4X-RAY DIFFRACTION4chain 'L' and (resid 112 through 218 )L0
5X-RAY DIFFRACTION5chain 'P' and (resid 1 through 6 )P0

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