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- PDB-3ifn: X-ray structure of amyloid beta peptide:antibody (Abeta1-40:12A11... -

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Basic information

Entry
Database: PDB / ID: 3ifn
TitleX-ray structure of amyloid beta peptide:antibody (Abeta1-40:12A11) complex
Components
  • 12A11 FAB antibody heavy chain
  • 12A11 FAB antibody light chain
  • Amyloid beta A4 protein
KeywordsIMMUNE SYSTEM / antibody / amyloid beta peptide
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 / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / 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 / axonogenesis / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / 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 / adult locomotory behavior / positive regulation of interleukin-1 beta production / endosome lumen / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / 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) / cellular response to amyloid-beta / positive regulation of inflammatory response / neuron projection development / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression / early endosome membrane / perikaryon / G alpha (i) signalling events / G alpha (q) signalling events / dendritic spine
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: 1.5 Å
AuthorsWeis, W.I. / Feinberg, H. / Basi, G.S. / Schenk, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural correlates of antibodies associated with acute reversal of amyloid beta-related behavioral deficits in a mouse model of Alzheimer disease.
Authors: Basi, G.S. / Feinberg, H. / Oshidari, F. / Anderson, J. / Barbour, R. / Baker, J. / Comery, T.A. / Diep, L. / Gill, D. / Johnson-Wood, K. / Goel, A. / Grantcharova, K. / Lee, M. / Li, J. / ...Authors: Basi, G.S. / Feinberg, H. / Oshidari, F. / Anderson, J. / Barbour, R. / Baker, J. / Comery, T.A. / Diep, L. / Gill, D. / Johnson-Wood, K. / Goel, A. / Grantcharova, K. / Lee, M. / Li, J. / Partridge, A. / Griswold-Prenner, I. / Piot, N. / Walker, D. / Widom, A. / Pangalos, M.N. / Seubert, P. / Jacobsen, J.S. / Schenk, D. / Weis, W.I.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 6, 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: 12A11 FAB antibody heavy chain
L: 12A11 FAB antibody light chain
P: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)52,4053
Polymers52,4053
Non-polymers00
Water8,467470
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-28 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.99, 87.01, 58.99
Angle α, β, γ (deg.)90.00, 95.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 12A11 FAB antibody heavy chain


Mass: 23978.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: CET1018 / Cell line (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): OVARY
#2: Antibody 12A11 FAB antibody light chain


Mass: 24090.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: CET1018 / Cell line (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): OVARY
#3: Protein/peptide Amyloid beta A4 protein


Mass: 4335.852 Da / Num. of mol.: 1 / Fragment: residues 672-711 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05067
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 5.3 mg/ml, 10 mM Hepes, pH 7.5, 75 mM NaCl. Protein:peptide molar ratio: 1:4.5. Reservoir: 0.2M NaCl, 25% Peg 4K, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→58.695 Å / Num. obs: 67740 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→58.695 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.22 / σ(F): 1.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 3440 5.08 %
Rwork0.187 --
obs0.1883 67712 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.95 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 101.97 Å2 / Biso mean: 20.925 Å2 / Biso min: 3.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.123 Å2
2--5.135 Å20 Å2
3----4.815 Å2
Refinement stepCycle: LAST / Resolution: 1.5→58.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 0 470 3859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053678
X-RAY DIFFRACTIONf_angle_d0.9945061
X-RAY DIFFRACTIONf_chiral_restr0.063583
X-RAY DIFFRACTIONf_plane_restr0.004644
X-RAY DIFFRACTIONf_dihedral_angle_d15.6391347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52060.24061500.20432269X-RAY DIFFRACTION89
1.5206-1.54230.25521420.20772511X-RAY DIFFRACTION95
1.5423-1.56530.23931210.19692555X-RAY DIFFRACTION98
1.5653-1.58980.22051390.19242603X-RAY DIFFRACTION98
1.5898-1.61580.23261290.18842512X-RAY DIFFRACTION98
1.6158-1.64370.22351590.18112570X-RAY DIFFRACTION98
1.6437-1.67360.20861120.1822580X-RAY DIFFRACTION98
1.6736-1.70580.22641140.17632580X-RAY DIFFRACTION98
1.7058-1.74060.21511350.17932563X-RAY DIFFRACTION98
1.7406-1.77850.2171400.18082575X-RAY DIFFRACTION98
1.7785-1.81980.2121390.18092547X-RAY DIFFRACTION98
1.8198-1.86530.23181370.1832568X-RAY DIFFRACTION98
1.8653-1.91580.20531420.18542556X-RAY DIFFRACTION98
1.9158-1.97220.21651400.19082588X-RAY DIFFRACTION98
1.9722-2.03580.23871390.19282564X-RAY DIFFRACTION99
2.0358-2.10860.23861380.18682585X-RAY DIFFRACTION98
2.1086-2.1930.25171210.18952591X-RAY DIFFRACTION99
2.193-2.29280.2151370.19182591X-RAY DIFFRACTION99
2.2928-2.41370.20331750.19762580X-RAY DIFFRACTION99
2.4137-2.56490.22271330.19222632X-RAY DIFFRACTION100
2.5649-2.7630.20731420.19852592X-RAY DIFFRACTION100
2.763-3.0410.20891350.19812634X-RAY DIFFRACTION100
3.041-3.4810.18581330.18172649X-RAY DIFFRACTION100
3.481-4.38550.18241330.15582629X-RAY DIFFRACTION99
4.3855-58.73950.1661550.14912648X-RAY DIFFRACTION99
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)
10.34140.2041-0.03230.54890.23751.6948-0.01260.0316-0.0585-0.0898-0.0041-0.012-0.0918-0.12380.01730.1090.0022-0.01540.0851-0.00220.09559.650867.686339.2134
20.99040.454-0.22070.78570.20930.68690.1558-0.18910.07090.0376-0.0874-0.0776-0.0999-0.0218-0.0388-0.0003-0.0050.01460.0372-0.04230.083530.567889.603263.2003
30.78230.2139-0.00850.45450.230.32650.03460.05620.0291-0.0618-0.0064-0.104-0.12080.0449-0.02760.15770.01070.02010.05290.00080.082723.445679.099225.9316
40.5249-0.3950.32660.797-0.06910.21590.0498-0.04160.0323-0.0776-0.02160.00760.02240.0025-0.01470.06460.0159-0.00490.10440.00860.095344.092184.580155.3393
52.4131-0.2046-2.77593.7367-0.39092.3834-0.29690.2821-0.15650.0682-0.0116-0.33260.4386-0.26670.27380.2157-0.02660.0180.1552-0.00140.181512.319662.187422.4043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain H and resid 1-120H1 - 120
2X-RAY DIFFRACTION2chain H and resid 121-222H121 - 222
3X-RAY DIFFRACTION3chain L and resid 1-112L1 - 112
4X-RAY DIFFRACTION4chain L and resid 113-219L113 - 219
5X-RAY DIFFRACTION5chain P and resid 2-7P2 - 7

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