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- PDB-5zv3: Crystal structure of human anti-tau antibody CBTAU-28.1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5zv3
TitleCrystal structure of human anti-tau antibody CBTAU-28.1 in complex with its tau peptide
Components
  • Heavy chain of antibody CBTAU28.1
  • Light chain (kappa) of antibody CBTAU28.1
  • Peptide from Microtubule-associated protein tau
KeywordsIMMUNE SYSTEM / antibody / tau protein / peptide antigen
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 / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding ...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 / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding / generation of neurons / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of chromosome organization / central nervous system neuron development / intracellular distribution of mitochondria / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / dynactin binding / regulation of microtubule polymerization / apolipoprotein binding / main axon / protein polymerization / axolemma / glial cell projection / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / neurofibrillary tangle assembly / positive regulation of axon extension / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / nuclear periphery / regulation of microtubule cytoskeleton organization / protein phosphatase 2A binding / cellular response to reactive oxygen species / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / protein homooligomerization / synapse organization / regulation of synaptic plasticity / PKR-mediated signaling / response to lead ion / SH3 domain binding / microtubule cytoskeleton organization / memory / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / cellular response to heat / microtubule cytoskeleton / cell body / growth cone / actin binding / double-stranded DNA binding / protein-macromolecule adaptor activity / microtubule binding / dendritic spine / sequence-specific DNA binding / amyloid fibril formation / microtubule / learning or memory / neuron projection / regulation of autophagy / membrane raft / negative regulation of gene expression / axon / neuronal cell body / DNA damage response / dendrite / 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
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsZhang, H. / Wilson, I.A.
CitationJournal: Acta Neuropathol Commun / Year: 2018
Title: A common antigenic motif recognized by naturally occurring human VH5-51/VL4-1 anti-tau antibodies with distinct functionalities.
Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / ...Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / Ameijde, J. / Inganas, H. / van Winsen, M. / Koldijk, M.H. / Zuijdgeest, D. / Borgers, M. / Dockx, K. / Stoop, E.J.M. / Yu, W. / Brinkman-van der Linden, E.C. / Ummenthum, K. / van Kolen, K. / Mercken, M. / Steinbacher, S. / de Marco, D. / Hoozemans, J.J. / Wilson, I.A. / Koudstaal, W. / Goudsmit, J.
History
DepositionMay 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 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: Peptide from Microtubule-associated protein tau
H: Heavy chain of antibody CBTAU28.1
L: Light chain (kappa) of antibody CBTAU28.1


Theoretical massNumber of molelcules
Total (without water)50,6893
Polymers50,6893
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-24 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.241, 49.423, 61.375
Angle α, β, γ (deg.)90.00, 105.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Peptide from Microtubule-associated protein tau / tau peptide


Mass: 2025.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#2: Antibody Heavy chain of antibody CBTAU28.1


Mass: 24420.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Light chain (kappa) of antibody CBTAU28.1


Mass: 24242.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.23 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085M Tris-HCl, pH 8.5, 0.17M sodium acetate, 25.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 25910 / % possible obs: 97.5 % / Redundancy: 3.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.08 / Rrim(I) all: 0.15 / Rsym value: 0.12 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3146 / CC1/2: 0.65 / Rpim(I) all: 0.65 / Rsym value: 0.86 / % possible all: 78.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QOT

3qot
PDB Unreleased entry


Resolution: 2.093→41.223 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.2508 1314 5.07 %
Rwork0.1873 --
obs0.1906 25909 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.093→41.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 0 247 3679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073515
X-RAY DIFFRACTIONf_angle_d0.9524788
X-RAY DIFFRACTIONf_dihedral_angle_d12.6712103
X-RAY DIFFRACTIONf_chiral_restr0.055529
X-RAY DIFFRACTIONf_plane_restr0.006614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0929-2.17670.32991110.24092234X-RAY DIFFRACTION80
2.1767-2.27570.28221290.21852714X-RAY DIFFRACTION97
2.2757-2.39570.2561440.20612785X-RAY DIFFRACTION100
2.3957-2.54580.29481560.2082790X-RAY DIFFRACTION100
2.5458-2.74230.2971410.20652779X-RAY DIFFRACTION100
2.7423-3.01820.31031790.2092780X-RAY DIFFRACTION100
3.0182-3.45470.25811580.18462788X-RAY DIFFRACTION100
3.4547-4.35180.23131490.16262826X-RAY DIFFRACTION100
4.3518-41.23070.18391470.16952899X-RAY DIFFRACTION100

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