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- PDB-7fgl: The complex structure of PHF core domain peptide of tau, VQIVYK, ... -

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Basic information

Entry
Database: PDB / ID: 7fgl
TitleThe complex structure of PHF core domain peptide of tau, VQIVYK, and antibody's Fab domain.
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • VQIVYK
KeywordsIMMUNE SYSTEM / tauopathies / tau protein / antibody / Alzheimer's disease / Fab domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / AMMONIUM ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTsuchida, T. / Tsuchiya, T. / Miyamoto, K. / In, Y. / Minoura, K. / Taniguchi, T. / Ishida, T. / Tomoo, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The cross-reaction complex structure with VQIVYK of tau and the antibody's Fab domain.
Authors: Tomohiro, T. / Takahiro, T. / Katsushiro, M. / Yasuko, I. / Katsuhiko, M. / Taizo, T. / Toshimitsu, I. / Koji, T.
History
DepositionJul 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab Heavy Chain
L: Fab Light Chain
C: VQIVYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9087
Polymers47,6143
Non-polymers2944
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-27 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.980, 70.720, 118.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide VQIVYK


Mass: 749.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab Heavy Chain


Mass: 23229.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab Light Chain


Mass: 23634.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 426 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19% PEG3350, 20% Glycerol, 0.2M Ammonium iodide, 0.01M Tris-HCl
PH range: 8 / Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.9→59.08 Å / Num. obs: 28351 / % possible obs: 99.4 % / Redundancy: 3.47 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.364 / Num. unique obs: 28351

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystalCleardata reduction
CrystalCleardata scaling
BALBESphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LRA

6lra


Resolution: 2.1→59.08 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.889 / SU B: 6.407 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26962 1518 5.1 %RANDOM
Rwork0.1997 ---
obs0.20317 28351 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å20 Å2
2---0.49 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.1→59.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 19 422 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133441
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173149
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6444686
X-RAY DIFFRACTIONr_angle_other_deg1.2231.5737314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7645441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56624.06133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27515546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.948158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
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_it2.6923.6971773
X-RAY DIFFRACTIONr_mcbond_other2.693.6971772
X-RAY DIFFRACTIONr_mcangle_it3.9885.5342211
X-RAY DIFFRACTIONr_mcangle_other3.9875.5342212
X-RAY DIFFRACTIONr_scbond_it2.8413.951668
X-RAY DIFFRACTIONr_scbond_other2.843.9491669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2645.7942476
X-RAY DIFFRACTIONr_long_range_B_refined6.36743.7173774
X-RAY DIFFRACTIONr_long_range_B_other6.36643.7133775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 108 -
Rwork0.284 2076 -
obs--99.82 %

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