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- PDB-6co3: aducanumab abeta complex -

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Basic information

Entry
Database: PDB / ID: 6co3
Titleaducanumab abeta complex
Components
  • ALA-GLU-PHE-ARG-HIS-ASP
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / antibody Fab fragment
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / intracellular copper ion homeostasis / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / response to interleukin-1 / cholesterol metabolic process / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / learning / dendritic shaft / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / serine-type endopeptidase inhibitor activity / visual learning / neuromuscular junction / recycling endosome / cognition / Golgi lumen / positive regulation of inflammatory response / neuron cellular homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / cellular response to amyloid-beta / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle / 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. / 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: 2.384 Å
AuthorsArndt, J.W.
CitationJournal: Sci Rep / Year: 2018
Title: Structural and kinetic basis for the selectivity of aducanumab for aggregated forms of amyloid-beta.
Authors: Arndt, J.W. / Qian, F. / Smith, B.A. / Quan, C. / Kilambi, K.P. / Bush, M.W. / Walz, T. / Pepinsky, R.B. / Bussiere, T. / Hamann, S. / Cameron, T.O. / Weinreb, P.H.
History
DepositionMar 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
Q: ALA-GLU-PHE-ARG-HIS-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0274
Polymers48,9313
Non-polymers961
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-47 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.659, 64.844, 67.280
Angle α, β, γ (deg.)90.00, 95.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab light chain


Mass: 23228.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab heavy chain


Mass: 24374.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide ALA-GLU-PHE-ARG-HIS-ASP


Mass: 1327.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: P05067*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 19% PEG 3350 in 100 mM sodium acetate, and 300 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 22692 / % possible obs: 93.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 9
Reflection shellResolution: 2.38→2.51 Å / Rmerge(I) obs: 0.281

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CNR

6cnr


Resolution: 2.384→19.955 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1125 4.96 %
Rwork0.1813 --
obs0.1839 22664 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.384→19.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 5 28 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033406
X-RAY DIFFRACTIONf_angle_d0.664631
X-RAY DIFFRACTIONf_dihedral_angle_d16.1512034
X-RAY DIFFRACTIONf_chiral_restr0.046518
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3843-2.49260.3341110.27392341X-RAY DIFFRACTION80
2.4926-2.62370.31031680.25332754X-RAY DIFFRACTION97
2.6237-2.78770.26841480.23342815X-RAY DIFFRACTION98
2.7877-3.00230.26141570.22142814X-RAY DIFFRACTION98
3.0023-3.30320.3411360.22222776X-RAY DIFFRACTION97
3.3032-3.77830.2521540.19542705X-RAY DIFFRACTION93
3.7783-4.74970.17781110.14042648X-RAY DIFFRACTION90
4.7497-19.9560.18881400.14772686X-RAY DIFFRACTION90
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)
13.4534-0.9521-0.40830.6408-0.26991.43320.0982-0.60510.77141.04180.0261-0.7423-0.50890.8449-0.18321.0435-0.2474-0.30350.7562-0.06260.705825.105239.2141-4.0723
21.5483-0.38460.12520.5994-0.10411.8198-0.0435-0.34640.14611.52620.0705-0.6931-0.240.7408-0.04051.048-0.1298-0.24550.7499-0.05390.516820.113731.5051-0.3032
33.5548-0.2923-0.46411.1182-0.15071.13450.1392-0.57970.24150.47820.034-1.0151-0.27650.9808-0.20150.6574-0.1133-0.24580.7456-0.05090.673227.931.9585-8.211
42.8361-0.1193-0.56552.4801-0.53930.9752-0.1272-0.186-0.33150.2369-0.1165-1.4915-0.10130.29990.14980.38020.0389-0.07080.6258-0.03011.507144.862820.8391-26.5272
51.1987-0.6315-0.58391.6218-0.41211.2141-0.0172-0.0586-0.06540.5272-0.01750.1701-0.0031-0.11910.10910.4809-0.0440.06670.424-0.00750.28115.138125.6008-17.6719
62.0762-1.1280.37273.31090.22253.201-0.06910.10620.10420.41710.1320.0899-0.4308-0.0788-0.04740.5134-0.03380.07120.52590.02350.29514.35334.055-19.0226
70.8304-0.12860.32210.58840.49451.30340.0278-0.00650.36140.47620.0486-0.0806-0.27540.0872-0.14650.5953-0.04470.08330.43270.01860.32588.122533.7771-14.5643
81.52580.0639-0.60250.8955-0.56071.61850.14070.323-0.49470.3194-0.2029-0.89260.1161-0.1620.0440.37160.0219-0.01020.3571-0.07430.803926.532416.032-26.0122
91.7552-1.15160.01110.81350.16351.85410.0292-0.2224-1.29060.23820.1183-0.65030.3685-0.0377-0.06170.47140.0663-0.0940.54620.06861.400733.53067.3485-25.5094
105.00520.7602-0.71184.3467-1.97358.64540.035-0.18961.279-0.2188-0.2995-0.4311-0.49440.72390.32561.2613-0.02910.03730.55540.0760.70955.816448.3385-10.4271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'L' and (resid 33 through 90 )
3X-RAY DIFFRACTION3chain 'L' and (resid 91 through 113 )
4X-RAY DIFFRACTION4chain 'L' and (resid 114 through 211 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 39 )
6X-RAY DIFFRACTION6chain 'H' and (resid 40 through 83 )
7X-RAY DIFFRACTION7chain 'H' and (resid 84 through 110 )
8X-RAY DIFFRACTION8chain 'H' and (resid 111 through 156 )
9X-RAY DIFFRACTION9chain 'H' and (resid 157 through 225 )
10X-RAY DIFFRACTION10chain 'Q' and (resid 2 through 7 )

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