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- PDB-5myo: Structure of Pyroglutamate-Abeta-specific Fab c#6 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5myo
TitleStructure of Pyroglutamate-Abeta-specific Fab c#6 in complex with human Abeta-pE3-12-PEGb
Components
  • Amyloid beta A4 protein
  • Fab c#6 heavy chain
  • Fab c#6 light chain
KeywordsIMMUNE SYSTEM / Alzheimer's disease / pyroglutamate Abeta / monoclonal antibody / fibrillation
Function / homology
Function and homology information


amyloid-beta complex / microglia development / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway ...amyloid-beta complex / microglia development / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / astrocyte activation involved in immune response / smooth endoplasmic reticulum calcium ion homeostasis / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / suckling behavior / COPII-coated ER to Golgi transport vesicle / positive regulation of protein metabolic process / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / forebrain development / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / axonogenesis / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / response to interleukin-1 / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / platelet alpha granule lumen / positive regulation of glycolytic process / adult locomotory behavior / dendritic shaft / positive regulation of long-term synaptic potentiation / central nervous system development / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / learning / locomotory behavior / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / synapse organization / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / 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 / Platelet degranulation / cell-cell junction
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 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 27, 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: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
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 2.2Nov 13, 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
A: Fab c#6 light chain
B: Fab c#6 heavy chain
C: Fab c#6 light chain
D: Fab c#6 heavy chain
E: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3049
Polymers98,9325
Non-polymers3724
Water20,8431157
1
A: Fab c#6 light chain
B: Fab c#6 heavy chain
E: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3576
Polymers50,0773
Non-polymers2803
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-42 kcal/mol
Surface area20390 Å2
MethodPISA
2
C: Fab c#6 light chain
D: Fab c#6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9473
Polymers48,8552
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-20 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.774, 65.958, 67.760
Angle α, β, γ (deg.)62.870, 82.930, 84.110
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Amyloid precursor protein / Beta-amyloid precursor protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 1222.264 Da / Num. of mol.: 1 / Fragment: UNP residues 674-683 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Fab c#6 light chain


Mass: 24169.971 Da / Num. of mol.: 2
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#6 heavy chain


Mass: 24684.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 3 types, 1161 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop
Details: 25.5% w/v PEG 4000 15% glycerol 170 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→27.189 Å / Num. obs: 99426 / % possible obs: 89.3 % / Observed criterion σ(I): -3 / Redundancy: 2.807 % / Biso Wilson estimate: 14.95 Å2 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.041 / Χ2: 0.984 / Net I/σ(I): 17.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.59-1.691.3610.3332.03101100.45854.3
1.69-1.791.9980.2393.42129940.31588.2
1.79-1.892.0880.1535.4108660.20192.6
1.89-1.992.1660.0998.2790910.12996
1.99-2.492.6230.05915.26275760.07499.3
2.49-2.993.8370.03828.54122110.04499.7
2.99-3.494.7350.02842.4261690.03299.7
3.49-3.994.70.02449.5234660.02799.6
3.99-4.494.7230.02253.6920900.02599.1
4.49-104.6360.02351.9644460.02699.1
10-204.4680.022553700.02595.9
20-304.2430.02254.89370.02686
27.189-30

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.15 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.19 Å
Translation2.5 Å27.19 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.1.4phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZEA

1zea


Resolution: 1.59→27.189 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 4972 5 %random
Rwork0.1776 ---
obs0.1796 99419 89.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 63.54 Å2 / Biso mean: 20.2986 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.59→27.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 0 23 1157 8011
Biso mean--33.71 29.83 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067244
X-RAY DIFFRACTIONf_angle_d0.869901
X-RAY DIFFRACTIONf_chiral_restr0.0541116
X-RAY DIFFRACTIONf_plane_restr0.0051264
X-RAY DIFFRACTIONf_dihedral_angle_d5.0275842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.59-1.60560.4324290.321754516
1.6056-1.62450.3432750.2653141740
1.6245-1.64430.29371080.2449206259
1.6443-1.66510.3161390.2345263175
1.6651-1.6870.26871550.2362295983
1.687-1.71020.26791580.226300087
1.7102-1.73460.25791660.2216316088
1.7346-1.76050.27771620.2151306089
1.7605-1.7880.30491690.2056322890
1.788-1.81730.25651660.2077314592
1.8173-1.84860.25541740.1996331293
1.8486-1.88220.23351740.1962329894
1.8822-1.91840.24721730.1989328995
1.9184-1.95760.24721770.1983336496
1.9576-2.00010.22261830.1876346897
2.0001-2.04660.21661790.1767341398
2.0466-2.09780.23961830.1776348199
2.0978-2.15450.21691860.17793522100
2.1545-2.21790.21561830.17583486100
2.2179-2.28940.21821860.17823530100
2.2894-2.37120.24351830.17993480100
2.3712-2.46610.21491860.1793539100
2.4661-2.57820.21821860.18453520100
2.5782-2.7140.22451850.18583515100
2.714-2.88390.21121850.17873519100
2.8839-3.10630.20111840.17613500100
3.1063-3.41830.20431840.16393503100
3.4183-3.91170.1751850.1513505100
3.9117-4.92360.15971850.13923515100
4.9236-27.1890.20311840.173348199

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