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- PDB-6pil: Antibody scFv-M204 monomeric state -

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Basic information

Entry
Database: PDB / ID: 6pil
TitleAntibody scFv-M204 monomeric state
ComponentsscFv-M204 antibody
KeywordsIMMUNE SYSTEM / anti-tau-oligomer scFv antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsAbskharon, R. / Sawaya, M.R. / Seidler, P.M. / Cascio, D. / Eisenberg, D.S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01 AG029430 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RF1 AG054022 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)1F32 NS095661 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1F32 NS095661 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structure of a conformational antibody that binds tau oligomers and inhibits pathological seeding by extracts from donors with Alzheimer's disease.
Authors: Abskharon, R. / Seidler, P.M. / Sawaya, M.R. / Cascio, D. / Yang, T.P. / Philipp, S. / Williams, C.K. / Newell, K.L. / Ghetti, B. / DeTure, M.A. / Dickson, D.W. / Vinters, H.V. / Felgner, P. ...Authors: Abskharon, R. / Seidler, P.M. / Sawaya, M.R. / Cascio, D. / Yang, T.P. / Philipp, S. / Williams, C.K. / Newell, K.L. / Ghetti, B. / DeTure, M.A. / Dickson, D.W. / Vinters, H.V. / Felgner, P.L. / Nakajima, R. / Glabe, C.G. / Eisenberg, D.S.
History
DepositionJun 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv-M204 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1684
Polymers27,0621
Non-polymers1063
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.420, 60.420, 159.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Antibody scFv-M204 antibody


Mass: 27061.957 Da / Num. of mol.: 1 / Fragment: scFv
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pMES4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2 M Lithium sulfate, 0.1 M Phosphate/Citrate pH 4.2, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.2→56.5 Å / Num. obs: 15422 / % possible obs: 97.9 % / Redundancy: 3.593 % / Biso Wilson estimate: 46.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.084 / Χ2: 1.08 / Net I/σ(I): 11.14 / Num. measured all: 55416 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.263.6530.6441.914091113111200.7360.75299
2.26-2.323.6920.5082.364098111411100.830.59699.6
2.32-2.393.610.4322.713830106810610.8440.50599.3
2.39-2.463.5280.3683.08352410369990.8930.43296.4
2.46-2.543.5720.3043.83601103410080.9250.35797.5
2.54-2.633.7720.2684.6236669819720.9260.31399.1
2.63-2.733.7860.2026.0835899549480.960.23599.4
2.73-2.843.7220.1687.0633879189100.9660.19799.1
2.84-2.973.6510.129.1131768778700.9890.1499.2
2.97-3.113.6130.09311.0930538608450.9920.10898.3
3.11-3.283.3860.07513.5526148127720.9930.08795.1
3.28-3.483.7110.06416.8928397727650.9940.07499.1
3.48-3.723.6440.05519.6626137267170.9950.06598.8
3.72-4.023.5430.04721.8924166936820.9970.05598.4
4.02-4.43.490.03825.821156206060.9980.04497.7
4.4-4.923.2930.03227.3817195795220.9980.03890.2
4.92-5.683.5320.03326.7418515335240.9990.03998.3
5.68-6.963.4510.03824.6315014474350.9980.04597.3
6.96-9.843.1220.02826.9710493623360.9990.03392.8
9.84-56.53.1090.02232.3468423322010.02794.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALE20180126data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→56.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.219 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1543 10.01 %RANDOM
Rwork0.194 ---
obs0.198 15421 97.9 %-
Displacement parametersBiso max: 124.68 Å2 / Biso mean: 42.9 Å2 / Biso min: 21.13 Å2
Baniso -1Baniso -2Baniso -3
1--5.0125 Å20 Å20 Å2
2---5.0125 Å20 Å2
3---10.025 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.2→56.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 3 105 1815
Biso mean--50.84 44.59 -
Num. residues----226
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d562SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes287HARMONIC5
X-RAY DIFFRACTIONt_it1750HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1991SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1750HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2387HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion16.06
LS refinement shellResolution: 2.2→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3719 31 10.03 %
Rwork0.2726 278 -
all0.2811 309 -
obs--97.19 %
Refinement TLS params.Method: refined / Origin x: 6.7207 Å / Origin y: 14.1659 Å / Origin z: 25.7847 Å
111213212223313233
T-0.0307 Å2-0.031 Å20.0097 Å2--0.0786 Å20.0131 Å2---0.0749 Å2
L0.9249 °2-0.4964 °2-0.2993 °2-1.3443 °20.7601 °2--2.569 °2
S-0.0271 Å °-0.0105 Å °0.074 Å °-0.13 Å °0.1085 Å °-0.0526 Å °-0.2047 Å °-0.0644 Å °-0.0814 Å °
Refinement TLS groupSelection details: { A|* }

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