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- PDB-6gk7: Crystal structure of anti-tau antibody dmCBTAU-27.1, double mutan... -

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Basic information

Entry
Database: PDB / ID: 6gk7
TitleCrystal structure of anti-tau antibody dmCBTAU-27.1, double mutant (S31Y, T100I) of CBTAU-27.1, in complex with Tau peptide A8119B (residues 299-318)
Components
  • (HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-27.1(S31Y,T100I)) x 2
  • HUMAN TAU PEPTIDE A8119 RESIDUES 299-318
KeywordsIMMUNE SYSTEM / ANTIBODY / FAB / TAU / COMPLEX
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 / 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 / lipoprotein particle binding / dynactin binding / glial cell projection / negative regulation of mitochondrial membrane potential / 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 / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / supramolecular fiber organization / stress granule assembly / regulation of cellular response to heat / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / axon cytoplasm / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / 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 / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cellular response to reactive oxygen species / microtubule cytoskeleton organization / SH3 domain binding / cytoplasmic ribonucleoprotein granule / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / microtubule cytoskeleton / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / single-stranded DNA binding / cellular response to heat / cell body / protein-folding chaperone binding / growth cone / microtubule binding / double-stranded DNA binding / microtubule / sequence-specific DNA binding / amyloid fibril formation / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / 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
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSteinbacher, S. / Mrosek, M. / Juraszek, J.
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 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-27.1(S31Y,T100I)
H: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-27.1(S31Y,T100I)
A: HUMAN TAU PEPTIDE A8119 RESIDUES 299-318
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4035
Polymers49,3323
Non-polymers712
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-54 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.829, 60.524, 91.048
Angle α, β, γ (deg.)90.00, 104.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-27.1(S31Y,T100I)


Mass: 24116.666 Da / Num. of mol.: 1 / Fragment: FAB ANTIBODY FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-27.1(S31Y,T100I)


Mass: 23952.826 Da / Num. of mol.: 1 / Fragment: FAB ANTIBODY FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide HUMAN TAU PEPTIDE A8119 RESIDUES 299-318


Mass: 1262.537 Da / Num. of mol.: 1 / Fragment: FAB ANTIBODY FRAGMENT / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→88.2 Å / Num. obs: 10377 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 9.5
Reflection shellResolution: 2.95→3.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.457 / % possible all: 98.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0151refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→88.2 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.86 / SU B: 0.465 / SU ML: 0.405 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26778 643 6.2 %RANDOM
Rwork0.22049 ---
obs0.22352 9734 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.321 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å20.29 Å2
2---2.09 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.95→88.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 2 32 3507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193472
X-RAY DIFFRACTIONr_bond_other_d0.0020.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9354739
X-RAY DIFFRACTIONr_angle_other_deg1.15137151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32424.493138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61315512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6571511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02793
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8193.0031797
X-RAY DIFFRACTIONr_mcbond_other0.8153.0021796
X-RAY DIFFRACTIONr_mcangle_it1.4255.0632241
X-RAY DIFFRACTIONr_mcangle_other1.4265.0642242
X-RAY DIFFRACTIONr_scbond_it0.783.0541675
X-RAY DIFFRACTIONr_scbond_other0.7763.0551675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3545.1312498
X-RAY DIFFRACTIONr_long_range_B_refined2.36625.8813411
X-RAY DIFFRACTIONr_long_range_B_other2.36425.8913409
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 43 -
Rwork0.338 706 -
obs--98.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.95351.5175-0.40871.1798-0.3140.11530.07210.14630.43070.06180.10280.32310.00050.0093-0.1750.40790.0879-0.03810.5437-0.04110.3401-29.2747.453-1.477
23.41171.7018-1.362.3274-0.94264.1421-0.35761.01660.2381-0.66040.36380.19890.20670.0288-0.00610.2293-0.0429-0.13250.49380.03390.2131-41.7730.70415.156
33.53390.21261.92131.85221.01992.2970.0062-0.3040.23930.3395-0.1121-0.01490.12770.03130.1060.0695-0.02750.02090.1059-0.00520.1548-40.691.29953.443
45.25791.75941.53713.14271.33073.7446-0.11091.5348-0.0734-0.49960.1717-0.4880.13060.7531-0.06070.14370.04940.06030.6372-0.01660.3002-20.1173.19718.429
50.69131.57760.08155.1528-0.85552.40220.0125-0.083-0.00580.2852-0.1139-0.2464-0.03910.21710.10150.05720.0304-0.06650.0613-0.00970.1614-27.942-6.21847.214
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A290 - 325
2X-RAY DIFFRACTION2L1 - 114
3X-RAY DIFFRACTION3L115 - 230
4X-RAY DIFFRACTION4H1 - 122
5X-RAY DIFFRACTION5H123 - 230

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