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- PDB-6dc9: Fab/epitope complex of human chimeric monoclonal antibody h4E6 ta... -

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Basic information

Entry
Database: PDB / ID: 6dc9
TitleFab/epitope complex of human chimeric monoclonal antibody h4E6 targeting a phosphorylated tau epitope.
Components
  • Fab heavy chain
  • Fab light chain
  • Microtubule-associated protein tau
KeywordsIMMUNE SYSTEM / monoclonal antibody / fab / tau / phosphorylation state -specific antibody
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of protein localization to synapse / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / positive regulation of protein localization to synapse / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression / tubulin complex / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / central nervous system neuron development / intracellular distribution of mitochondria / regulation of microtubule polymerization / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / negative regulation of mitochondrial membrane potential / apolipoprotein binding / glial cell projection / axolemma / protein polymerization / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / neurofibrillary tangle assembly / Activation of AMPK downstream of NMDARs / synapse assembly / regulation of cellular response to heat / supramolecular fiber organization / positive regulation of protein localization / regulation of calcium-mediated signaling / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / cytoplasmic microtubule organization / axon cytoplasm / positive regulation of microtubule polymerization / stress granule assembly / phosphatidylinositol binding / regulation of microtubule cytoskeleton organization / nuclear periphery / protein phosphatase 2A binding / positive regulation of superoxide anion generation / cellular response to reactive oxygen species / astrocyte activation / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to lead ion / synapse organization / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / actin binding / cellular response to heat / microtubule cytoskeleton / cell body / growth cone / double-stranded DNA binding / microtubule binding / protein-macromolecule adaptor activity / dendritic spine / sequence-specific DNA binding / microtubule / amyloid fibril formation / learning or memory / neuron projection / regulation of autophagy / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.999 Å
AuthorsChukwu, J.E. / Kong, X.-P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS077239 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG032611 United States
CitationJournal: MAbs / Year: 2019
Title: Structural characterization of monoclonal antibodies targeting C-terminal Ser404region of phosphorylated tau protein.
Authors: Chukwu, J.E. / Congdon, E.E. / Sigurdsson, E.M. / Kong, X.P.
History
DepositionMay 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: 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_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 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: Fab heavy chain
L: Fab light chain
P: Microtubule-associated protein tau
I: Fab heavy chain
M: Fab light chain
Q: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3839
Polymers100,1006
Non-polymers2823
Water905
1
H: Fab heavy chain
L: Fab light chain
P: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2375
Polymers50,0503
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-47 kcal/mol
Surface area19130 Å2
MethodPISA
2
I: Fab heavy chain
M: Fab light chain
Q: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1454
Polymers50,0503
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-42 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.212, 65.080, 97.439
Angle α, β, γ (deg.)90.00, 112.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 2 molecules PQ

#3: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 3430.589 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636

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Antibody , 2 types, 4 molecules HILM

#1: Antibody Fab heavy chain


Mass: 23135.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 23484.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Hek-293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25.5% polyethylene glycol 4000 and 0.17 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.99→48.69 Å / Num. obs: 18575 / % possible obs: 99.38 % / Redundancy: 3.8 % / Net I/σ(I): 10.15
Reflection shellResolution: 2.99→3.11 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.999→48.692 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 1859 9.96 %
Rwork0.2021 --
obs0.208 35852 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.999→48.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6597 0 16 5 6618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026770
X-RAY DIFFRACTIONf_angle_d0.5959231
X-RAY DIFFRACTIONf_dihedral_angle_d11.9824050
X-RAY DIFFRACTIONf_chiral_restr0.0411048
X-RAY DIFFRACTIONf_plane_restr0.0081175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9994-3.04050.3531460.31351278X-RAY DIFFRACTION98
3.0405-3.0840.33761370.29921259X-RAY DIFFRACTION99
3.084-3.130.35761320.28971330X-RAY DIFFRACTION99
3.13-3.17890.37211420.29011275X-RAY DIFFRACTION99
3.1789-3.2310.36261580.27321276X-RAY DIFFRACTION99
3.231-3.28670.3261270.27141300X-RAY DIFFRACTION99
3.2867-3.34640.33241500.26371278X-RAY DIFFRACTION99
3.3464-3.41080.28471430.24631316X-RAY DIFFRACTION99
3.4108-3.48040.32861410.23181279X-RAY DIFFRACTION99
3.4804-3.5560.30361380.23921281X-RAY DIFFRACTION99
3.556-3.63870.30161310.22471333X-RAY DIFFRACTION99
3.6387-3.72970.24891440.22121243X-RAY DIFFRACTION99
3.7297-3.83050.28791560.22411334X-RAY DIFFRACTION99
3.8305-3.94320.28871290.20921265X-RAY DIFFRACTION99
3.9432-4.07040.28641400.2151307X-RAY DIFFRACTION99
4.0704-4.21580.25011450.19081266X-RAY DIFFRACTION99
4.2158-4.38450.24441470.16221310X-RAY DIFFRACTION100
4.3845-4.58390.23111410.15831305X-RAY DIFFRACTION99
4.5839-4.82540.191440.15131256X-RAY DIFFRACTION100
4.8254-5.12740.2311470.15451323X-RAY DIFFRACTION100
5.1274-5.52280.25531480.16251267X-RAY DIFFRACTION100
5.5228-6.07760.24681480.16841315X-RAY DIFFRACTION100
6.0776-6.95490.25441400.19841306X-RAY DIFFRACTION100
6.9549-8.75410.22521470.17411293X-RAY DIFFRACTION100
8.7541-48.69810.15891500.16821286X-RAY DIFFRACTION99

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