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- PDB-6bb4: Fab/epitope complex of mouse monoclonal antibody C5.2 targeting a... -

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Basic information

Entry
Database: PDB / ID: 6bb4
TitleFab/epitope complex of mouse monoclonal antibody C5.2 targeting a phospho-tau epitope.
Components
  • Microtubule-associated protein tau
  • Mouse monoclonal antibody C5.2 Fab heavy chain
  • Mouse monoclonal antibody C5.2 Fab light chain
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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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: Sci Rep / Year: 2018
Title: Tau Antibody Structure Reveals a Molecular Switch Defining a Pathological Conformation of the Tau Protein.
Authors: Chukwu, J.E. / Pedersen, J.T. / Pedersen, L.O. / Volbracht, C. / Sigurdsson, E.M. / Kong, X.P.
History
DepositionOct 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 30, 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
L: Mouse monoclonal antibody C5.2 Fab light chain
H: Mouse monoclonal antibody C5.2 Fab heavy chain
P: Microtubule-associated protein tau
M: Mouse monoclonal antibody C5.2 Fab light chain
I: Mouse monoclonal antibody C5.2 Fab heavy chain
Q: Microtubule-associated protein tau
N: Mouse monoclonal antibody C5.2 Fab light chain
J: Mouse monoclonal antibody C5.2 Fab heavy chain
R: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,08212
Polymers149,7979
Non-polymers2853
Water15,745874
1
L: Mouse monoclonal antibody C5.2 Fab light chain
H: Mouse monoclonal antibody C5.2 Fab heavy chain
P: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0274
Polymers49,9323
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-40 kcal/mol
Surface area20530 Å2
MethodPISA
2
M: Mouse monoclonal antibody C5.2 Fab light chain
I: Mouse monoclonal antibody C5.2 Fab heavy chain
Q: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0274
Polymers49,9323
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-41 kcal/mol
Surface area20410 Å2
MethodPISA
3
N: Mouse monoclonal antibody C5.2 Fab light chain
J: Mouse monoclonal antibody C5.2 Fab heavy chain
R: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0274
Polymers49,9323
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-40 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.156, 40.535, 228.064
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-569-

HOH

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Components

#1: Antibody Mouse monoclonal antibody C5.2 Fab light chain


Mass: 23574.035 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Mouse monoclonal antibody C5.2 Fab heavy chain


Mass: 23728.580 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 2629.664 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25.5% polyethylene glycol 4000, 0.17 M ammonium sulfate, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2015
Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.099→44.25 Å / Num. obs: 84763 / % possible obs: 99.51 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06924 / Rpim(I) all: 0.03851 / Rrim(I) all: 0.07945 / Net I/σ(I): 12.34
Reflection shellResolution: 2.099→2.174 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5445 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 8330 / CC1/2: 0.89 / Rpim(I) all: 0.3028 / Rrim(I) all: 0.6245 / % possible all: 99.32

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASER1.12_2829phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→44.25 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2699 --
Rwork0.2176 --
obs-84763 99.51 %
Refinement stepCycle: LAST / Resolution: 2.099→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10005 0 15 874 10894

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