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- PDB-5my4: Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5my4
TitleStructure of Pyroglutamate-Abeta-specific Fab c#17 in complex with human Abeta-pE3-12PEGb
Components
  • Fab c#17 heavy chain
  • Fab c#17 light chain
  • Pyroglutamate-Abeta pE3-12-PEGb
KeywordsIMMUNE SYSTEM / Alzheimer's disease / pyroglutamate Abeta / monoclonal antibody / fibrillation
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 / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / transition metal ion binding / main axon / intracellular copper ion homeostasis / regulation of multicellular organism growth / 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 / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / 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 / endosome lumen / positive regulation of interleukin-1 beta production / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / adult locomotory behavior / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / synapse organization / recycling endosome / visual learning / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.211 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 25, 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 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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 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
A: Fab c#17 light chain
B: Fab c#17 heavy chain
C: Pyroglutamate-Abeta pE3-12-PEGb


Theoretical massNumber of molelcules
Total (without water)49,9513
Polymers49,9513
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-31 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.170, 87.142, 58.029
Angle α, β, γ (deg.)90.000, 96.060, 90.000
Int Tables number4
Space group name H-MP1211

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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 Pyroglutamate-Abeta pE3-12-PEGb


Mass: 1222.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% w/v PEG 3350, 100 mM bis-Tris, 200 mM magnesium chloride, 0.5% n-dodecyl-beta-D-maltoside

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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: Feb 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→28.852 Å / Num. obs: 40703 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 8.868 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.092 / Χ2: 0.959 / Net I/σ(I): 18.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.21-2.313.3550.2594.5541190.30686.8
2.31-2.414.9550.2426.4522140.27199.3
2.41-2.517.2280.2328.4618700.25100
2.51-2.6110.4140.21811.5216050.22999.9
2.61-310.8790.15715.4344330.16599.9
3-3.3910.620.09622.5926360.10199.9
3.39-3.7810.2730.06829.3716420.072100
3.78-4.1710.2860.05932.7110990.06299.9
4.17-4.5610.2550.05137.177530.05499.6
4.56-1010.3720.0538.5822370.05399.6
10-209.5930.04245.422140.04599.5
20-308.4760.04146.23210.04495.5
28.852-30

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.85 Å
Translation2.5 Å28.85 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DQT

2dqt


Resolution: 2.211→28.852 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 27.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 2042 5.02 %random
Rwork0.1862 ---
obs0.1894 40700 96.85 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 64.01 Å2 / Biso mean: 23.984 Å2 / Biso min: 9.77 Å2
Refinement stepCycle: final / Resolution: 2.211→28.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 0 191 3566
Biso mean---26.1 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083463
X-RAY DIFFRACTIONf_angle_d0.9884716
X-RAY DIFFRACTIONf_chiral_restr0.055527
X-RAY DIFFRACTIONf_plane_restr0.006600
X-RAY DIFFRACTIONf_dihedral_angle_d7.7252048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2112-2.26260.3298960.24141816191268
2.2626-2.31920.2921290.22672424255392
2.3192-2.38190.3361390.22482598273797
2.3819-2.45190.34811400.230526492789100
2.4519-2.5310.27241430.218126842827100
2.531-2.62140.28391380.21526392777100
2.6214-2.72630.27511370.212326632800100
2.7263-2.85030.31331390.211826802819100
2.8503-3.00040.2851380.213126222760100
3.0004-3.18820.25811410.188826262767100
3.1882-3.4340.2541410.177926722813100
3.434-3.77890.22551410.16812640278199
3.7789-4.32410.18741420.154526552797100
4.3241-5.4420.17731400.14212654279499
5.442-28.85490.24341380.17562636277499

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