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- PDB-6dca: Fab/epitope complex of mouse monoclonal antibody 6B2 targeting a ... -

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Basic information

Entry
Database: PDB / ID: 6dca
TitleFab/epitope complex of mouse monoclonal antibody 6B2 targeting a non-phosphorylated tau epitope.
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Microtubule-associated protein tauTau protein
KeywordsIMMUNE SYSTEM / monoclonal antibody / fab / tau / phosphorylation state-specific antibody
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / lipoprotein particle binding / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / apolipoprotein binding / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / stress granule assembly / cytoplasmic microtubule organization / regulation of cellular response to heat / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / protein-macromolecule adaptor activity / single-stranded DNA binding / cell-cell signaling / cellular response to heat / cell body / actin binding / growth cone / protein-folding chaperone binding / double-stranded DNA binding / microtubule binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / dendrite / neuronal cell body / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding
Similarity search - Function
: / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / 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 / Resolution: 2.599 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
P: Microtubule-associated protein tau
M: Fab light chain
I: Fab heavy chain
Q: Microtubule-associated protein tau
N: Fab light chain
J: Fab heavy chain
R: Microtubule-associated protein tau
O: Fab light chain
K: Fab heavy chain
S: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,76416
Polymers204,38412
Non-polymers3804
Water5,441302
1
L: Fab light chain
H: Fab heavy chain
P: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1914
Polymers51,0963
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-35 kcal/mol
Surface area19550 Å2
MethodPISA
2
M: Fab light chain
I: Fab heavy chain
Q: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1914
Polymers51,0963
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-34 kcal/mol
Surface area19490 Å2
MethodPISA
3
N: Fab light chain
J: Fab heavy chain
R: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1914
Polymers51,0963
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-34 kcal/mol
Surface area19340 Å2
MethodPISA
4
O: Fab light chain
K: Fab heavy chain
S: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1914
Polymers51,0963
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-36 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.010, 59.704, 143.846
Angle α, β, γ (deg.)89.43, 92.69, 97.35
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Fab light chain / Fragment antigen-binding


Mass: 23982.711 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
Fab heavy chain / Fragment antigen-binding


Mass: 23844.688 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide
Microtubule-associated protein tau / Tau protein / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 3268.639 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.602→45.605 Å / Num. obs: 53304 / % possible obs: 97.6 % / Redundancy: 1.8 % / Net I/σ(I): 5.84
Reflection shellResolution: 2.602→2.69 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.599→45.605 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1980 3.75 %
Rwork0.1887 --
obs0.1914 52861 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→45.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13340 0 20 302 13662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913688
X-RAY DIFFRACTIONf_angle_d1.118660
X-RAY DIFFRACTIONf_dihedral_angle_d16.0418184
X-RAY DIFFRACTIONf_chiral_restr0.0542136
X-RAY DIFFRACTIONf_plane_restr0.0072348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5992-2.66420.33431270.24323586X-RAY DIFFRACTION96
2.6642-2.73620.37191550.25113631X-RAY DIFFRACTION96
2.7362-2.81670.33671410.24723651X-RAY DIFFRACTION97
2.8167-2.90760.32931430.24673597X-RAY DIFFRACTION97
2.9076-3.01150.3261360.23733699X-RAY DIFFRACTION96
3.0115-3.1320.31551440.21543634X-RAY DIFFRACTION97
3.132-3.27450.28911410.1983621X-RAY DIFFRACTION97
3.2745-3.44710.26551390.18833638X-RAY DIFFRACTION97
3.4471-3.6630.22031510.17793644X-RAY DIFFRACTION97
3.663-3.94570.24521370.16093638X-RAY DIFFRACTION96
3.9457-4.34250.22931430.1573602X-RAY DIFFRACTION96
4.3425-4.97020.21231420.14423632X-RAY DIFFRACTION96
4.9702-6.25930.20641330.17363661X-RAY DIFFRACTION97
6.2593-45.61210.24331480.19613647X-RAY DIFFRACTION97

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