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- PDB-5v7u: Cyrstal structure of anti-Tau antibody CBTAU-22.1 Fab -

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Basic information

Entry
Database: PDB / ID: 5v7u
TitleCyrstal structure of anti-Tau antibody CBTAU-22.1 Fab
Components
  • CBTAU-22.1 Fab heavy chain
  • CBTAU-22.1 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: 1.64 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 30, 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-22.1 Fab light chain
H: CBTAU-22.1 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1744
Polymers47,9822
Non-polymers1922
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-63 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.467, 67.229, 62.470
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody CBTAU-22.1 Fab light chain


Mass: 24089.922 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-22.1 Fab heavy chain


Mass: 23891.828 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M citrate buffer, pH 4.0, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 53078 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rpim(I) all: 0.05 / Rsym value: 0.08 / Net I/σ(I): 23.7
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 3.5 % / CC1/2: 0.684 / Rpim(I) all: 0.41 / Rsym value: 0.66 / % 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: 4LRI, 4JPK

4lri

4jpk


Resolution: 1.64→45.691 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.2165 2696 5.08 %
Rwork0.1761 --
obs0.1781 53050 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→45.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 10 462 3787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073453
X-RAY DIFFRACTIONf_angle_d1.2084702
X-RAY DIFFRACTIONf_dihedral_angle_d13.451265
X-RAY DIFFRACTIONf_chiral_restr0.045525
X-RAY DIFFRACTIONf_plane_restr0.006605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6352-1.66490.34481170.28592213X-RAY DIFFRACTION84
1.6649-1.6970.32951440.26722669X-RAY DIFFRACTION100
1.697-1.73160.27821270.23512664X-RAY DIFFRACTION100
1.7316-1.76930.26071390.21812657X-RAY DIFFRACTION100
1.7693-1.81040.27841530.20262683X-RAY DIFFRACTION100
1.8104-1.85570.22161540.19412633X-RAY DIFFRACTION100
1.8557-1.90590.26951400.1892647X-RAY DIFFRACTION100
1.9059-1.96190.26061370.18642701X-RAY DIFFRACTION100
1.9619-2.02530.23931150.18382707X-RAY DIFFRACTION100
2.0253-2.09770.21151420.17962632X-RAY DIFFRACTION100
2.0977-2.18160.2241540.17342690X-RAY DIFFRACTION100
2.1816-2.28090.19891240.17422674X-RAY DIFFRACTION100
2.2809-2.40120.20761440.18032682X-RAY DIFFRACTION100
2.4012-2.55160.24911380.1932656X-RAY DIFFRACTION100
2.5516-2.74860.21691310.18482703X-RAY DIFFRACTION100
2.7486-3.02520.21481630.17832667X-RAY DIFFRACTION100
3.0252-3.46280.20051520.16072673X-RAY DIFFRACTION100
3.4628-4.36220.1891550.14342692X-RAY DIFFRACTION100
4.3622-45.70840.191670.16132711X-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)
12.1419-0.3784-1.25652.84821.03844.01990.0576-0.07710.04370.0470.0098-0.1047-0.02920.0454-0.07230.09730.0012-0.00920.1099-0.01330.1059.398311.47422.2825
20.52340.21170.96980.09740.35641.13230.0337-0.0224-0.0390.0083-0.0280.01290.0112-0.0697-0.03480.15440.0054-0.00090.1499-0.02030.1519-4.63998.5119.7638
34.2892-0.05550.02221.7381-0.4181.54640.00150.22050.0696-0.13710.10330.1361-0.1365-0.1248-0.10430.17750.0142-0.0240.1271-0.04020.1235-18.107610.5933-6.2687
47.0767-2.89573.09764.7173-1.89514.36980.23540.1985-0.4519-0.1306-0.03550.31050.13060.0682-0.17780.0827-0.02670.00820.1299-0.01010.1511-15.50242.044130.1755
50.87270.30920.27450.70110.39982.11240.0122-0.0218-0.02330.0875-0.06250.0691-0.0331-0.06090.0450.09680.01740.01760.12160.00160.1333-10.10726.067232.0161
61.44360.7837-0.66210.6895-0.43585.04560.1225-0.04260.1242-0.0794-0.1241-0.0875-0.292-0.26-0.00510.13330.02630.010.1122-0.02350.1755-17.9252-0.68494.6852
73.6841-2.1081-2.45836.94874.7615.0346-0.27050.1008-0.28150.2452-0.28770.19120.8579-0.48780.43750.2267-0.04860.07680.1103-0.02290.2103-21.8148-9.62794.0701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 75 )
2X-RAY DIFFRACTION2chain 'L' and (resid 76 through 128 )
3X-RAY DIFFRACTION3chain 'L' and (resid 129 through 214 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 17 )
5X-RAY DIFFRACTION5chain 'H' and (resid 18 through 136 )
6X-RAY DIFFRACTION6chain 'H' and (resid 137 through 197 )
7X-RAY DIFFRACTION7chain 'H' and (resid 198 through 228 )

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