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- PDB-5myk: Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5myk
TitleStructure of Pyroglutamate-Abeta-specific Fab c#17 in complex with murine Abeta-pE3-18PEGb
Components
  • Amyloid beta A4 protein
  • Fab c#17 heavy chain
  • Fab c#17 light chain
KeywordsIMMUNE SYSTEM / Alzheimer's disease / pyroglutamate Abeta / monoclonal antibody / fibrillation
Function / homology
Function and homology information


Formyl peptide receptors bind formyl peptides and many other ligands / Advanced glycosylation endproduct receptor signaling / ECM proteoglycans / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / TAK1-dependent IKK and NF-kappa-B activation / G alpha (q) signalling events ...Formyl peptide receptors bind formyl peptides and many other ligands / Advanced glycosylation endproduct receptor signaling / ECM proteoglycans / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / TRAF6 mediated NF-kB activation / Lysosome Vesicle Biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / TAK1-dependent IKK and NF-kappa-B activation / G alpha (q) signalling events / G alpha (i) signalling events / Platelet degranulation / Mitochondrial protein degradation / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / synaptic assembly at neuromuscular junction / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / neuron remodeling / nuclear envelope lumen / intracellular vesicle / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / presynaptic active zone / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / 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 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / adult locomotory behavior / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / memory / positive regulation of interleukin-6 production / long-term synaptic potentiation / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / neuron differentiation / 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 / mitotic cell cycle / regulation of translation / heparin binding / regulation of gene expression / growth cone / cytoplasmic vesicle / neuron apoptotic process / gene expression / dendritic spine / perikaryon / response to oxidative stress
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. / 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 ...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. / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsParthier, C. / Piechotta, A. / Stubbs, M.T.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and functional analyses of pyroglutamate-amyloid-beta-specific antibodies as a basis for Alzheimer immunotherapy.
Authors: Piechotta, A. / Parthier, C. / Kleinschmidt, M. / Gnoth, K. / Pillot, T. / Lues, I. / Demuth, H.U. / Schilling, S. / Rahfeld, J.U. / Stubbs, M.T.
History
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 11, 2020Group: Atomic model / Data collection / Polymer sequence / Category: atom_site / entity_poly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 17, 2024Group: 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 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab c#17 light chain
B: Fab c#17 heavy chain
C: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)50,6003
Polymers50,6003
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-34 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.915, 42.943, 57.979
Angle α, β, γ (deg.)83.850, 83.340, 90.300
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab c#17 light chain


Mass: 24080.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab c#17 heavy chain


Mass: 24648.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein/peptide Amyloid beta A4 protein / ABPP / APP / Alzheimer disease amyloid A4 protein homolog / Amyloid precursor protein / ...ABPP / APP / Alzheimer disease amyloid A4 protein homolog / Amyloid precursor protein / Amyloidogenic glycoprotein / AG / Beta-amyloid precursor protein


Mass: 1871.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P12023
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES Sodium Salt 0.2M Calcium Acetate 18% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→19.326 Å / Num. obs: 48637 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 1.993 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.042 / Χ2: 0.956 / Net I/σ(I): 16.33 / Num. measured all: 96945 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.71.9870.4131.9880190.7510.58493.7
1.7-1.81.9940.2513.2364090.8840.35694.5
1.8-1.91.9940.155.3251190.9560.21395.1
1.9-21.9960.0878.941320.9820.12494.8
2-2.51.9940.04416.06122530.9950.06395.2
2.5-31.9940.02328.8754310.9980.03295.6
3-3.51.9950.01640.7227210.9990.02393.9
3.5-41.9950.01546.7715150.9990.02193.5
4-4.51.9970.01452.869110.9990.0292.6
4.5-101.9960.01451.4719690.9990.01993.6
10-201.9940.01555.491580.9980.02185.4
20-30
19.326-30

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.36 Å19.33 Å
Translation6.36 Å19.33 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MY4

5my4


Resolution: 1.6→19.326 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.95
RfactorNum. reflection% reflection
Rfree0.2098 2433 5 %
Rwork0.1726 --
obs0.1745 48636 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.89 Å2 / Biso mean: 25.6257 Å2 / Biso min: 10.71 Å2
Refinement stepCycle: final / Resolution: 1.6→19.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 0 392 3773
Biso mean---34.31 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063484
X-RAY DIFFRACTIONf_angle_d0.8574749
X-RAY DIFFRACTIONf_chiral_restr0.054530
X-RAY DIFFRACTIONf_plane_restr0.005606
X-RAY DIFFRACTIONf_dihedral_angle_d6.0012454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63260.3261400.28422640278092
1.6326-1.66810.28221420.27112711285395
1.6681-1.70690.33391450.25032739288494
1.7069-1.74960.26641410.23352690283194
1.7496-1.79680.27371440.22512726287095
1.7968-1.84970.23561440.21212746289095
1.8497-1.90930.26831420.19952697283995
1.9093-1.97750.22891450.1872753289895
1.9775-2.05660.25851440.18612734287895
2.0566-2.15010.2361450.17952747289295
2.1501-2.26330.23851430.17882722286595
2.2633-2.40480.23351440.18152739288395
2.4048-2.59010.23161440.18482747289196
2.5901-2.850.2061440.17182733287796
2.85-3.26070.2011430.16922717286094
3.2607-4.10170.17431410.13992682282393
4.1017-19.3270.14631420.13592680282293
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)
14.8256-0.2172-0.30761.3481-0.4771.6990.07510.1174-0.2134-0.1269-0.0193-0.08090.74940.10370.01950.38710.0561-0.03590.18060.00960.20722.0469-11.6256-1.3157
21.5104-0.46160.54631.4622-0.46792.21690.0382-0.1421-0.1396-0.21970.05970.05020.4558-0.1336-0.03060.1928-0.0236-0.03640.1424-0.01050.1433-5.5172-2.4553-3.9197
30.979-0.93120.31531.0914-0.57722.02160.0397-0.02230.0815-0.2169-0.1255-0.18260.37150.11150.01640.19130.017-0.00870.1239-0.0020.1362.2045-2.3165-6.5987
40.7191-0.71270.54410.9978-0.76190.55950.14920.16780.1062-0.2677-0.1814-0.0610.3330.02940.04950.1814-0.0055-0.00230.20310.00910.16781.1773-10.41483.2464
51.32740.1608-1.14440.8539-0.20082.1020.09050.15490.07820.0733-0.0031-0.085-0.1046-0.1955-0.07120.18170.0218-0.0040.12720.00330.13926.9974-24.58325.462
60.872-0.0433-0.20530.7281-0.161.95920.0545-0.01520.03380.05750.0710.0932-0.0895-0.1514-0.1190.1168-0.01110.02160.17730.01030.1615-12.19628.99829.4629
71.0448-0.62490.45661.3608-0.21461.0699-0.1210.0824-0.15730.26130.065-0.09970.06640.04750.01740.2056-0.00740.02510.1383-0.01540.20816.0784-9.700630.3832
81.1769-0.4667-0.38711.24440.38221.4274-0.0744-0.0498-0.0170.04940.0358-0.1643-0.04920.14280.02020.2029-0.00220.01390.1214-0.02540.24814.2371-10.217731.3671
92.02050.8207-0.81060.95010.42372.0258-0.03150.18280.1442-0.2480.10950.1171-0.1375-0.0788-0.11640.14750.0004-0.04250.34210.05810.1992-19.273212.9627-3.1707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 53 )A19 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 95 )A54 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 118 )A96 - 118
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 219 )A119 - 219
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 112 )B1 - 112
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 154 )B113 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 222 )B155 - 222
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 6 )C2 - 6

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