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- PDB-6dcv: Crystal structure of human anti-tau antibody CBTAU-27.1 -

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Basic information

Entry
Database: PDB / ID: 6dcv
TitleCrystal structure of human anti-tau antibody CBTAU-27.1
Components
  • Light chain of CBTAU27.1 Fab
  • heavy chain of CBTAU-27.1 Fab
KeywordsIMMUNE SYSTEM / Tau / Fab / naturally occurring human antibody / common motif
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhu, X. / Zhang, H. / Wilson, I.A.
CitationJournal: Acta Neuropathol Commun / Year: 2018
Title: A common antigenic motif recognized by naturally occurring human VH5-51/VL4-1 anti-tau antibodies with distinct functionalities.
Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / ...Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / Ameijde, J. / Inganas, H. / van Winsen, M. / Koldijk, M.H. / Zuijdgeest, D. / Borgers, M. / Dockx, K. / Stoop, E.J.M. / Yu, W. / Brinkman-van der Linden, E.C. / Ummenthum, K. / van Kolen, K. / Mercken, M. / Steinbacher, S. / de Marco, D. / Hoozemans, J.J. / Wilson, I.A. / Koudstaal, W. / Goudsmit, J.
History
DepositionMay 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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 1.3Oct 16, 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: Light chain of CBTAU27.1 Fab
H: heavy chain of CBTAU-27.1 Fab
A: Light chain of CBTAU27.1 Fab
B: heavy chain of CBTAU-27.1 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0867
Polymers98,8104
Non-polymers2763
Water11,476637
1
L: Light chain of CBTAU27.1 Fab
H: heavy chain of CBTAU-27.1 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5894
Polymers49,4052
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-31 kcal/mol
Surface area20040 Å2
MethodPISA
2
A: Light chain of CBTAU27.1 Fab
B: heavy chain of CBTAU-27.1 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4973
Polymers49,4052
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-32 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.411, 60.578, 169.472
Angle α, β, γ (deg.)90.00, 103.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-467-

HOH

21H-446-

HOH

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Components

#1: Antibody Light chain of CBTAU27.1 Fab


Mass: 24432.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: P01834*PLUS
#2: Antibody heavy chain of CBTAU-27.1 Fab


Mass: 24971.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: P01857*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes, pH 7.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 72579 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rpim(I) all: 0.05 / Rsym value: 0.12 / Net I/σ(I): 17.3
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 3509 / CC1/2: 0.78 / Rpim(I) all: 0.48 / Rsym value: 0.82

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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: 3QOS

3qos
PDB Unreleased entry


Resolution: 1.9→46.533 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.53
RfactorNum. reflection% reflection
Rfree0.2286 3644 5.03 %
Rwork0.186 --
obs0.1881 72457 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6852 0 18 637 7507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077045
X-RAY DIFFRACTIONf_angle_d1.1699563
X-RAY DIFFRACTIONf_dihedral_angle_d13.7272508
X-RAY DIFFRACTIONf_chiral_restr0.0471060
X-RAY DIFFRACTIONf_plane_restr0.0051222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8971-1.9220.2981230.29462458X-RAY DIFFRACTION92
1.922-1.94840.34181180.2712550X-RAY DIFFRACTION97
1.9484-1.97620.33581240.26572614X-RAY DIFFRACTION98
1.9762-2.00570.27761360.25612572X-RAY DIFFRACTION97
2.0057-2.0370.28551340.24012612X-RAY DIFFRACTION98
2.037-2.07040.27951530.22692614X-RAY DIFFRACTION98
2.0704-2.10610.23741480.21662572X-RAY DIFFRACTION99
2.1061-2.14440.2581310.22092693X-RAY DIFFRACTION99
2.1444-2.18570.25721520.21442586X-RAY DIFFRACTION100
2.1857-2.23030.28691390.20662694X-RAY DIFFRACTION100
2.2303-2.27880.22611220.20062632X-RAY DIFFRACTION100
2.2788-2.33180.231530.20582699X-RAY DIFFRACTION100
2.3318-2.39010.28761470.20952620X-RAY DIFFRACTION100
2.3901-2.45470.28581340.19842649X-RAY DIFFRACTION100
2.4547-2.52690.25551740.20012679X-RAY DIFFRACTION100
2.5269-2.60850.23681370.1972650X-RAY DIFFRACTION100
2.6085-2.70170.24031450.18952629X-RAY DIFFRACTION100
2.7017-2.80990.21671300.19212692X-RAY DIFFRACTION100
2.8099-2.93770.2481420.18862705X-RAY DIFFRACTION100
2.9377-3.09260.24161650.18952655X-RAY DIFFRACTION100
3.0926-3.28630.21921310.18162674X-RAY DIFFRACTION100
3.2863-3.540.22021410.16772671X-RAY DIFFRACTION100
3.54-3.8960.22371330.15552686X-RAY DIFFRACTION100
3.896-4.45940.17541450.14632694X-RAY DIFFRACTION100
4.4594-5.61690.161430.14292735X-RAY DIFFRACTION100
5.6169-46.54710.21711440.18812778X-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)
12.31070.5118-0.8541.9675-0.72365.2327-0.05170.30820.039-0.59020.12940.1974-0.2465-0.0997-0.0210.5026-0.0409-0.11340.33280.02470.2779-6.4944-15.140750.9122
21.7445-0.0872-0.74091.0229-0.11572.2355-0.06790.4326-0.0435-0.78160.14590.0930.03820.013-0.04450.4929-0.0549-0.03410.3423-0.01060.165-1.8824-22.187752.663
34.17111.25433.10792.11441.47384.97430.0475-0.0609-0.03960.2472-0.0196-0.05070.05590.1058-0.02140.16980.00520.03410.1812-0.00630.1658-1.6899-23.677187.3764
41.64710.78220.97562.30511.71283.86640.0879-0.20390.03960.2922-0.1114-0.0250.0431-0.12150.02450.2422-0.010.01360.2333-0.00530.1982-0.9684-17.959689.598
53.77480.85953.71761.91791.15075.10150.1007-0.6640.3810.4672-0.2670.19270.1929-0.31250.12840.2952-0.01720.08610.421-0.0740.1981-7.5153-19.567496.4098
67.49110.51072.9327.05660.80415.0870.3211-0.8378-1.30970.97490.1433-0.55671.0889-0.3564-0.39970.5924-0.06710.0020.41090.1140.31920.0718-25.8836104.2698
71.6145-0.2210.00181.38960.14062.75870.0160.4142-0.4079-0.43530.0469-0.54770.31680.1084-0.06110.3962-0.03590.16450.3578-0.07410.38818.1437-20.002258.5004
81.9544-0.36070.23361.34610.38962.00820.02390.9134-0.0243-0.95770.0819-0.5286-0.33140.4233-0.10990.6004-0.08560.23640.6378-0.07620.433918.889-16.461352.3053
90.37060.0305-0.0582.4487-0.55760.8039-0.0074-0.04370.00850.0899-0.0654-0.2223-0.06650.08410.0640.1749-0.0031-0.00140.2373-0.00160.20649.8645-26.419582.8809
103.54583.042-2.20425.9809-6.35817.3493-0.22440.2325-0.0552-0.3418-0.272-1.38270.02440.21830.46550.25580.02730.03720.29420.01590.518221.3671-25.867780.5643
113.35071.40751.19161.9467-2.41266.60430.11-1.01970.31861.67620.22430.48010.179-0.019-0.28430.93130.08070.10650.45980.05270.28179.6983-36.069298.6511
122.2072-0.3854-1.58342.76231.48134.95320.0838-0.515-0.0640.38940.1785-0.171-0.07290.2802-0.26950.33090.0716-0.1340.3903-0.07180.321333.4587-41.017231.5126
131.576-0.0787-0.6361.31270.32162.0221-0.0194-0.4288-0.01080.51070.0914-0.09390.1015-0.0713-0.08650.37410.0837-0.05650.3861-0.04620.200728.8485-48.065829.7307
143.8435-1.27193.40521.8239-1.32065.05970.14210.1092-0.0001-0.2171-0.06630.00430.1597-0.0115-0.04550.1491-0.00250.01840.16110.01080.254728.5619-49.7364-5.0356
151.583-0.76511.09931.8847-1.86244.43770.0460.17380.1285-0.2569-0.0143-0.035-0.0033-0.0054-0.01780.206-0.0017-0.0150.1510.02050.248227.8383-44.0486-7.2232
165.7698-1.42514.67352.6822-1.45976.61630.0660.69860.3162-0.4984-0.2493-0.27070.07910.37870.14420.20660.02110.05630.21070.05570.237534.4289-45.6572-14.0365
175.18120.10281.51738.1460.76034.77390.1250.4683-0.965-0.94760.29690.6370.4745-0.0415-0.14270.52090.0342-0.05710.3711-0.01660.294326.9038-51.9912-21.7852
183.2999-0.00950.21392.2267-0.15332.986-0.0191-0.5394-0.22210.41380.03610.48440.3834-0.2527-0.00940.33030.0030.11830.33180.00370.38218.8121-45.900923.9799
193.4557-0.3230.52171.8967-0.31773.0060.1214-0.94390.04980.92820.0480.6623-0.2639-0.3531-0.14150.5140.00560.18310.5491-0.03490.45848.1442-42.285630.1214
200.7695-0.2689-0.40221.83250.76421.0790.04530.05930.0486-0.1109-0.06730.0623-0.0365-0.10360.01950.15840.0013-0.03570.16770.00880.310117.0342-52.5077-0.4751
211.6159-2.2938-1.46845.97375.025.54230.01550.1028-0.60870.315-0.29591.52120.1155-0.46930.51810.1944-0.0453-0.03280.2688-0.05250.52475.4485-51.97581.8425
224.3231-2.09930.49145.9522.4671.5303-0.00051.32640.3306-1.20290.1746-0.43240.6149-0.097-0.23390.4385-0.07280.03810.43640.02630.350717.0893-62.0318-16.1368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 28)
2X-RAY DIFFRACTION2chain 'L' and (resid 29 through 104 )
3X-RAY DIFFRACTION3chain 'L' and (resid 105 through 144 )
4X-RAY DIFFRACTION4chain 'L' and (resid 145 through 186 )
5X-RAY DIFFRACTION5chain 'L' and (resid 187 through 206 )
6X-RAY DIFFRACTION6chain 'L' and (resid 207 through 214 )
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 47 )
8X-RAY DIFFRACTION8chain 'H' and (resid 48 through 101 )
9X-RAY DIFFRACTION9chain 'H' and (resid 102 through 210 )
10X-RAY DIFFRACTION10chain 'H' and (resid 211 through 221 )
11X-RAY DIFFRACTION11chain 'H' and (resid 222 through 231 )
12X-RAY DIFFRACTION12chain 'A' and (resid 1 through 28)
13X-RAY DIFFRACTION13chain 'A' and (resid 29 through 104 )
14X-RAY DIFFRACTION14chain 'A' and (resid 105 through 144 )
15X-RAY DIFFRACTION15chain 'A' and (resid 145 through 186 )
16X-RAY DIFFRACTION16chain 'A' and (resid 187 through 206 )
17X-RAY DIFFRACTION17chain 'A' and (resid 207 through 214 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 47 )
19X-RAY DIFFRACTION19chain 'B' and (resid 48 through 101 )
20X-RAY DIFFRACTION20chain 'B' and (resid 102 through 210 )
21X-RAY DIFFRACTION21chain 'B' and (resid 211 through 221 )
22X-RAY DIFFRACTION22chain 'B' and (resid 222 through 231 )

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