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- PDB-5mp1: Crystal structure of DC8E8 Fab in the complex with a 14-mer tau p... -

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Basic information

Entry
Database: PDB / ID: 5mp1
TitleCrystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 7.5
Components
  • Microtubule-associated protein tau
  • antibody Fab heavy chain
  • antibody Fab light chain
KeywordsIMMUNE SYSTEM / Antibody Fab / complex / tau protein
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 / supramolecular fiber organization / cellular response to brain-derived neurotrophic factor stimulus / 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 / synapse organization / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / SH3 domain binding / response to lead ion / 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 / actin binding / microtubule cytoskeleton / cell body / growth cone / 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 / 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
Microtubule-associated protein tau
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsSkrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
CitationJournal: To be published
Title: Crystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 7.5
Authors: Skrabana, R. / Novak, M.
History
DepositionDec 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Polymer sequence / Refinement description / Category: entity_poly / refine_hist
Item: _entity_poly.pdbx_seq_one_letter_code_can / _refine_hist.d_res_high
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 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
H: antibody Fab heavy chain
L: antibody Fab light chain
A: Microtubule-associated protein tau
C: antibody Fab heavy chain
D: antibody Fab light chain
B: Microtubule-associated protein tau
F: antibody Fab heavy chain
G: antibody Fab light chain
E: Microtubule-associated protein tau
J: antibody Fab heavy chain
K: antibody Fab light chain
I: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)197,78112
Polymers197,78112
Non-polymers00
Water00
1
C: antibody Fab heavy chain
D: antibody Fab light chain
B: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)49,4453
Polymers49,4453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-28 kcal/mol
Surface area19170 Å2
MethodPISA
2
F: antibody Fab heavy chain
G: antibody Fab light chain
E: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)49,4453
Polymers49,4453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-28 kcal/mol
Surface area19020 Å2
MethodPISA
3
J: antibody Fab heavy chain
K: antibody Fab light chain
I: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)49,4453
Polymers49,4453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-29 kcal/mol
Surface area18920 Å2
MethodPISA
4
H: antibody Fab heavy chain
L: antibody Fab light chain
A: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)49,4453
Polymers49,4453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-28 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.370, 82.370, 89.800
Angle α, β, γ (deg.)88.120, 84.780, 89.930
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
antibody Fab heavy chain


Mass: 23800.617 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
antibody Fab light chain


Mass: 24172.787 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 / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1471.722 Da / Num. of mol.: 4 / Fragment: UNP Residues 615-628 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 4000; 10% 2-Propanol, 0.1 M Na-HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.882
11-H, K, -L20.118
ReflectionResolution: 3.1→39.83 Å / Num. obs: 24488 / % possible obs: 78.4 % / Observed criterion σ(I): -3 / Redundancy: 1.722 % / Biso Wilson estimate: 30.496 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.64
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
3.1-3.181.5710.3132.670.741160.2
3.18-3.271.6120.2573.220.802172.9
3.27-3.361.660.2213.920.853183.5
3.36-3.471.7030.1695.310.917182.5
3.47-3.581.6870.145.890.944183.2
3.58-3.711.7140.1256.770.957181.3
3.71-3.851.7130.1197.170.954182.8
3.85-41.7090.0988.610.97181.6
4-4.181.7310.07610.590.981181.7
4.18-4.381.7360.06711.720.987181
4.38-4.621.7440.05213.60.992180.5
4.62-4.91.7750.05214.30.99180.1
4.9-5.241.7670.05314.340.992179.6
5.24-5.661.7830.05813.690.988179.3
5.66-6.21.7910.06511.60.988178.7
6.2-6.931.8190.06611.620.987177.5
6.93-81.8290.04316.260.995177.4
8-9.81.8420.02724.210.998175.7
9.8-13.861.8630.0229.270.999175.6
13.86-39.831.9080.02626.930.998149.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4OZ4

4oz4
PDB Unreleased entry


Resolution: 3.1→39.83 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.799 / SU B: 27.786 / SU ML: 0.492 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1257 5.1 %RANDOM
Rwork0.2221 ---
obs0.2245 23219 71.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.59 Å2 / Biso mean: 41.823 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1--9.02 Å215.35 Å2-1.75 Å2
2---19.15 Å2-12.31 Å2
3---28.17 Å2
Refinement stepCycle: final / Resolution: 3.1→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13383 0 0 0 13383
Num. residues----1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213723
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212430
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.94418664
X-RAY DIFFRACTIONr_angle_other_deg0.969328816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85451742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29724.302523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.182152174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6611547
X-RAY DIFFRACTIONr_chiral_restr0.0740.22096
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115403
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023040
LS refinement shellResolution: 3.1→3.189 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20

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