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- PDB-5v7r: Cyrstal structure of anti-Tau antibody CBTAU-7.1 Fab -

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Basic information

Entry
Database: PDB / ID: 5v7r
TitleCyrstal structure of anti-Tau antibody CBTAU-7.1 Fab
Components
  • CBTAU-7.1 Fab heavy chain
  • CBTAU-7.1 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / tau protein / alzheimer's disease
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, X. / Zhang, H. / Wilson, I.A.
CitationJournal: Acta Neuropathol. / Year: 2017
Title: Immunological memory to hyperphosphorylated tau in asymptomatic individuals.
Authors: Pascual, G. / Wadia, J.S. / Zhu, X. / Keogh, E. / Kukrer, B. / van Ameijde, J. / Inganas, H. / Siregar, B. / Perdok, G. / Diefenbach, O. / Nahar, T. / Sprengers, I. / Koldijk, M.H. / der ...Authors: Pascual, G. / Wadia, J.S. / Zhu, X. / Keogh, E. / Kukrer, B. / van Ameijde, J. / Inganas, H. / Siregar, B. / Perdok, G. / Diefenbach, O. / Nahar, T. / Sprengers, I. / Koldijk, M.H. / der Linden, E.C. / Peferoen, L.A. / Zhang, H. / Yu, W. / Li, X. / Wagner, M. / Moreno, V. / Kim, J. / Costa, M. / West, K. / Fulton, Z. / Chammas, L. / Luckashenak, N. / Fletcher, L. / Holland, T. / Arnold, C. / Anthony Williamson, R. / Hoozemans, J.J. / Apetri, A. / Bard, F. / Wilson, I.A. / Koudstaal, W. / Goudsmit, J.
History
DepositionMar 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Oct 4, 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 1.3Oct 23, 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
L: CBTAU-7.1 Fab light chain
H: CBTAU-7.1 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,0402
Polymers48,0402
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-25 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.903, 83.903, 109.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody CBTAU-7.1 Fab light chain


Mass: 23588.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#2: Antibody CBTAU-7.1 Fab heavy chain


Mass: 24452.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.01 Å3/Da / Density % sol: 69.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M ammonium dihydrogen phosphate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.3→39.171 Å / Num. obs: 33665 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rsym value: 0.07 / Net I/σ(I): 52.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.9 / CC1/2: 0.821 / Rpim(I) all: 0.34 / Rsym value: 0.79 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QEG, 3FN0

3qeg

3fn0


Resolution: 2.3→39.171 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1704 5.07 %
Rwork0.1713 --
obs0.174 33608 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 0 87 3396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093393
X-RAY DIFFRACTIONf_angle_d1.2324606
X-RAY DIFFRACTIONf_dihedral_angle_d14.3811213
X-RAY DIFFRACTIONf_chiral_restr0.046514
X-RAY DIFFRACTIONf_plane_restr0.005593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.36251280.27972660X-RAY DIFFRACTION100
2.3677-2.44410.30151600.25662631X-RAY DIFFRACTION100
2.4441-2.53140.28411430.24462659X-RAY DIFFRACTION100
2.5314-2.63280.30941260.24512655X-RAY DIFFRACTION100
2.6328-2.75260.30911410.25022669X-RAY DIFFRACTION100
2.7526-2.89760.27311420.22262669X-RAY DIFFRACTION100
2.8976-3.07910.2581470.22572628X-RAY DIFFRACTION100
3.0791-3.31670.24081410.21012648X-RAY DIFFRACTION100
3.3167-3.65030.27281500.1972678X-RAY DIFFRACTION100
3.6503-4.1780.22241400.16412667X-RAY DIFFRACTION100
4.178-5.26180.15211450.11152663X-RAY DIFFRACTION100
5.2618-39.1770.18281410.1232677X-RAY DIFFRACTION99
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)
11.5504-1.5541.89524.2737-0.30643.43910.27930.7463-0.9280.06960.15140.20110.48060.1978-0.36330.4379-0.105-0.01530.8124-0.22370.527613.7301-40.7193-11.8193
27.6275-2.22792.22873.69440.07433.1192-0.11971.6591-0.0968-0.5970.121-0.2196-0.11660.7138-0.03030.6007-0.131-0.05451.09620.00640.511811.4637-31.1931-19.0056
32.5316-1.9582.18064.52280.083.13660.08161.5306-0.3005-0.332-0.1407-0.29080.20850.646-0.26660.5845-0.08510.01771.3964-0.17330.572620.8011-37.1052-17.4333
47.5676-2.02322.45563.1390.01042.3731-0.54451.42190.0281-0.13470.63910.60430.17560.2486-0.0160.454-0.1562-0.04910.81780.1080.56966.3047-30.63-11.4699
58.5509-1.83143.07680.3075-0.69811.14670.35521.0525-0.94240.0824-0.2320.09330.2797-0.23150.19170.4613-0.05170.00360.6886-0.17730.502530.507-39.4104-6.2011
64.2585-1.3692-0.8812.2982-0.55644.8076-0.0991-0.27990.29370.2336-0.098-0.1634-0.5919-0.23740.21230.4809-0.0479-0.0340.3695-0.06280.347237.0804-29.696612.8584
73.6096-1.8630.44813.2472-2.62265.8132-0.4411-0.58610.02120.52420.18240.0759-0.658-0.44880.16170.5028-0.04010.03480.4579-0.05770.410732.5252-34.828919.0012
84.8584-0.1844-0.18523.45960.73315.9215-0.1258-0.00690.28920.0098-0.1943-0.1166-1.039-0.38780.17610.4834-0.0235-0.03680.3024-0.05370.391233.8183-29.263510.5216
94.7336-0.751-0.41094.07521.03558.82440.0814-0.29830.08780.9038-0.2357-0.3420.51420.69130.2090.4654-0.0448-0.05730.4045-0.00420.455343.401-35.718415.8633
104.88730.63851.01093.74551.7843.4575-0.64150.74061.7949-0.36160.21850.8926-0.5210.1910.33730.5071-0.1233-0.19340.67950.17861.18655.6762-14.974-7.1131
118.74211.2730.08242.23370.73333.82380.0991-0.63380.6531-0.0096-0.0928-0.0838-0.18830.08590.17510.7248-0.0267-0.05840.3978-0.12780.545935.1593-19.626911.2829
126.5823-0.4999-0.65232.53981.46133.72390.01810.17190.9591-0.14-0.19930.0166-0.6582-0.16970.09060.670.0445-0.05030.319-0.02510.528734.3599-16.5715.9678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'L' and (resid 26 through 69 )
3X-RAY DIFFRACTION3chain 'L' and (resid 70 through 83 )
4X-RAY DIFFRACTION4chain 'L' and (resid 84 through 101 )
5X-RAY DIFFRACTION5chain 'L' and (resid 102 through 113 )
6X-RAY DIFFRACTION6chain 'L' and (resid 114 through 150 )
7X-RAY DIFFRACTION7chain 'L' and (resid 151 through 163 )
8X-RAY DIFFRACTION8chain 'L' and (resid 164 through 188 )
9X-RAY DIFFRACTION9chain 'L' and (resid 189 through 214 )
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 111 )
11X-RAY DIFFRACTION11chain 'H' and (resid 112 through 147 )
12X-RAY DIFFRACTION12chain 'H' and (resid 148 through 229 )

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