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- PDB-6psc: Antibody scFv-M204 trimeric state -

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Basic information

Entry
Database: PDB / ID: 6psc
TitleAntibody scFv-M204 trimeric state
ComponentsscFv-M204 antibody
KeywordsIMMUNE SYSTEM / anti-tau-oligomer scFv antibody
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 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
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 12, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv-M204 antibody
B: scFv-M204 antibody
C: scFv-M204 antibody


Theoretical massNumber of molelcules
Total (without water)81,1863
Polymers81,1863
Non-polymers00
Water00
1
A: scFv-M204 antibody


Theoretical massNumber of molelcules
Total (without water)27,0621
Polymers27,0621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: scFv-M204 antibody


Theoretical massNumber of molelcules
Total (without water)27,0621
Polymers27,0621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: scFv-M204 antibody


Theoretical massNumber of molelcules
Total (without water)27,0621
Polymers27,0621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.160, 60.160, 526.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 2 - 232 / Label seq-ID: 2 - 245

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody scFv-M204 antibody


Mass: 27061.957 Da / Num. of mol.: 3 / 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

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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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.5 M Ammonium sulfate, 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.6→65.8 Å / Num. obs: 10789 / % possible obs: 87.4 % / Redundancy: 2.28 % / Biso Wilson estimate: 50.434 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.24 / Rrim(I) all: 0.303 / Χ2: 0.922 / Net I/σ(I): 3.69 / Num. measured all: 24601
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
3.6-3.692.220.9230.9317658737950.4581.17291.1
3.69-3.792.1020.8170.9916318577760.6521.04290.5
3.79-3.92.3390.7191.4517198237350.610.90189.3
3.9-4.032.3480.5391.7318488427870.7880.6893.5
4.03-4.162.3370.3962.3516227566940.8610.49891.8
4.16-4.32.2860.2893.1216058017020.9110.36787.6
4.3-4.472.3350.2883.1115347156570.9210.36291.9
4.47-4.652.2470.2113.9914817426590.9510.26888.8
4.65-4.852.3180.1794.5712986605600.9710.22484.8
4.85-5.092.120.1854.4312216745760.9580.23685.5
5.09-5.372.4450.1854.6713696435600.9520.22987.1
5.37-5.692.3640.1954.3912535955300.9440.24489.1
5.69-6.092.4350.1974.2412325975060.9550.24584.8
6.09-6.572.4070.1914.5511055264590.9380.23787.3
6.57-7.22.180.1874.279225004230.9440.23684.6
7.2-8.052.1170.1165.688324533930.9840.14886.8
8.05-9.32.3380.0788.458304183550.9940.09684.9
9.3-11.382.2610.0739.996673692950.990.08979.9
11.38-16.12.1010.069.774372992080.9930.07469.6
16.1-65.81.9330.0699.462301951190.9940.08461

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PK8

6pk8


Resolution: 3.6→65.8 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.867 / SU B: 101.953 / SU ML: 0.607 / SU R Cruickshank DPI: 0.6456 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.797
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 1079 10 %RANDOM
Rwork0.2516 ---
obs0.2545 9710 87.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 173.94 Å2 / Biso mean: 86.286 Å2 / Biso min: 54.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 3.6→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 0 0 5103
Num. residues----675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135232
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174680
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6537137
X-RAY DIFFRACTIONr_angle_other_deg1.2671.56510887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33822.286210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28815801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6511521
X-RAY DIFFRACTIONr_chiral_restr0.0540.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021113
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A69710.05
12B69710.05
21A69370.05
22C69370.05
31B69850.03
32C69850.03
LS refinement shellResolution: 3.6→3.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 79 -
Rwork0.381 715 -
all-794 -
obs--91.16 %
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)
10.7415-0.5126-0.04830.58660.07521.4293-0.0051-0.3118-0.0215-0.32990.2099-0.07470.0443-0.1879-0.20490.502-0.00770.02950.27840.00370.305425.12182.403251.3722
20.63980.2854-0.87282.22880.88831.97840.03120.04690.00140.07340.0873-0.17130.0611-0.0262-0.11850.3601-0.008-0.02110.3601-0.00770.309631.317711.31970.161
30.81040.46240.67020.7930.28171.437-0.03120.0690.09210.02940.07050.0109-0.072-0.0593-0.03930.48660.02310.00390.30020.00970.259526.746138.504240.4895
40.62310.82470.23121.4577-0.10271.5952-0.079-0.0254-0.2115-0.3322-0.0145-0.4211-0.0489-0.05610.09350.59170.00920.15480.3295-0.00420.158837.46929.272324.1093
51.73890.80170.10581.43320.54270.46130.13610.43050.04990.1387-0.03870.0432-0.0295-0.0042-0.09740.68-0.01-0.03430.3892-0.01310.059211.322117.92067.5596
61.1155-0.5203-0.27870.4070.23282.65850.077-0.1603-0.0745-0.1990.24060.00310.0574-0.0933-0.31760.4917-0.0371-0.10870.2852-0.04230.237715.372910.284927.4337
700000000000000-00.3819000.381900.3819000
800000000000000-00.3819000.381900.3819000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 119
2X-RAY DIFFRACTION2A120 - 232
3X-RAY DIFFRACTION3B2 - 119
4X-RAY DIFFRACTION4B120 - 232
5X-RAY DIFFRACTION5C2 - 119
6X-RAY DIFFRACTION6C120 - 232
7X-RAY DIFFRACTION7D2 - 119
8X-RAY DIFFRACTION8D120 - 232

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