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- PDB-6h0e: FAB dmCBTAU-22.1 IN COMPLEX WITH TAU PEPTIDE V1088-23 -

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Basic information

Entry
Database: PDB / ID: 6h0e
TitleFAB dmCBTAU-22.1 IN COMPLEX WITH TAU PEPTIDE V1088-23
Components
  • (HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1) x 2
  • Microtubule-associated protein tau
KeywordsIMMUNE SYSTEM / FAB / Tau peptide / complex
Function / homology
Function and homology information


Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of intracellular transport / positive regulation of long-term synaptic depression / regulation of microtubule-based movement / PKR-mediated signaling / axon extension / axo-dendritic transport / adult walking behavior / mitochondrion transport along microtubule / intrinsic apoptotic signaling pathway in response to oxidative stress ...Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of intracellular transport / positive regulation of long-term synaptic depression / regulation of microtubule-based movement / PKR-mediated signaling / axon extension / axo-dendritic transport / adult walking behavior / mitochondrion transport along microtubule / intrinsic apoptotic signaling pathway in response to oxidative stress / tubulin complex / main axon / negative regulation of tubulin deacetylation / axoneme / glial cell projection / intracellular transport / mRNA transport / positive regulation of axon extension / axonal growth cone / regulation of cellular response to heat / heat shock protein binding / positive regulation of microtubule polymerization / response to nutrient / axonogenesis / protein phosphatase 2A binding / regulation of autophagy / response to lead ion / neuron migration / Hsp90 protein binding / positive regulation of neuron projection development / microtubule cytoskeleton organization / cytoplasmic side of plasma membrane / microtubule cytoskeleton / neuron projection development / protein-folding chaperone binding / growth cone / cell body / microtubule binding / microtubule / postsynaptic density / neuron projection / membrane raft / axon / neuronal cell body / DNA damage response / dendrite / protein-containing complex binding / protein kinase binding / enzyme binding / DNA binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJuraszek, J. / Steinbacher, S.
CitationJournal: Acta Neuropathol Commun / Year: 2018
Title: Enhancement of therapeutic potential of a naturally occurring human antibody targeting a phosphorylated Ser422containing epitope on pathological tau.
Authors: van Ameijde, J. / Crespo, R. / Janson, R. / Juraszek, J. / Siregar, B. / Verveen, H. / Sprengers, I. / Nahar, T. / Hoozemans, J.J. / Steinbacher, S. / Willems, R. / Delbroek, L. / Borgers, M. ...Authors: van Ameijde, J. / Crespo, R. / Janson, R. / Juraszek, J. / Siregar, B. / Verveen, H. / Sprengers, I. / Nahar, T. / Hoozemans, J.J. / Steinbacher, S. / Willems, R. / Delbroek, L. / Borgers, M. / Dockx, K. / Van Kolen, K. / Mercken, M. / Pascual, G. / Koudstaal, W. / Apetri, A.
History
DepositionJul 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Database references / Polymer sequence / Category: citation / entity_poly
Item: _citation.country / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Oct 23, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
L: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
A: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
B: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
C: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
D: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
E: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
F: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
I: Microtubule-associated protein tau
G: Microtubule-associated protein tau
J: Microtubule-associated protein tau
K: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,20617
Polymers201,74512
Non-polymers4605
Water15,583865
1
H: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
L: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
I: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5284
Polymers50,4363
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-36 kcal/mol
Surface area20520 Å2
MethodPISA
2
A: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
B: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
K: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6205
Polymers50,4363
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-36 kcal/mol
Surface area20300 Å2
MethodPISA
3
C: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
D: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
G: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5284
Polymers50,4363
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-36 kcal/mol
Surface area20410 Å2
MethodPISA
4
E: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
F: HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1
J: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5284
Polymers50,4363
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-38 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.551, 95.502, 108.317
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
HUMAN FAB ANTIBODY FRAGMENT OF dmCBTAU-22.1


Mass: 23787.764 Da / Num. of mol.: 4 / 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 dmCBTAU-22.1


Mass: 23986.779 Da / Num. of mol.: 4 / 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
Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 2661.729 Da / Num. of mol.: 4 / Fragment: FAB ANTIBODY FRAGMENT / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P10637
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 % (w/v) PEG8K, 0.10 M Tris/HCl pH=7.0, 0.20 M Mg2Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.95→99.97 Å / Num. obs: 137233 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.44 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→99.97 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.675 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 1866 1.4 %RANDOM
Rwork0.22188 ---
obs0.22271 135351 93.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20.71 Å2
2---0.54 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→99.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13545 0 30 865 14440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01913883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212721
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.95618912
X-RAY DIFFRACTIONr_angle_other_deg2.729329381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17251770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36923.665543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.822152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3531574
X-RAY DIFFRACTIONr_chiral_restr0.1190.22112
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02115741
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023129
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_it7.2444.6627107
X-RAY DIFFRACTIONr_mcbond_other7.2434.6617106
X-RAY DIFFRACTIONr_mcangle_it8.1237.8078865
X-RAY DIFFRACTIONr_mcangle_other8.1237.8088866
X-RAY DIFFRACTIONr_scbond_it8.8715.1356776
X-RAY DIFFRACTIONr_scbond_other8.8715.1356776
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.5758.37310047
X-RAY DIFFRACTIONr_long_range_B_refined11.36520.84814659
X-RAY DIFFRACTIONr_long_range_B_other11.39320.81114453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 157 -
Rwork0.326 10509 -
obs--98.18 %

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