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- PDB-6dg2: Antigen Binding Fragment of the Pan-ebolavirus Monoclonal Antibody 6D6 -

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Basic information

Entry
Database: PDB / ID: 6dg2
TitleAntigen Binding Fragment of the Pan-ebolavirus Monoclonal Antibody 6D6
Components
  • 6D6 Fab heavy chain
  • 6D6 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Monoclonal / Antigen Binding Fragment / Fab / Ebola
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMilligan, J.C. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U19AI109762-05 United States
CitationJournal: J Infect Dis / Year: 2019
Title: Structural Characterization of Pan-Ebolavirus Antibody 6D6 Targeting the Fusion Peptide of the Surface Glycoprotein.
Authors: Jacob C Milligan / Diptiben V Parekh / Katherine M Fuller / Manabu Igarashi / Ayato Takada / Erica Ollmann Saphire /
Abstract: Ebola virus infection causes severe disease in humans and represents a global health threat. Candidates for immunotherapeutics and vaccines have shown promise in clinical trials, although they are ...Ebola virus infection causes severe disease in humans and represents a global health threat. Candidates for immunotherapeutics and vaccines have shown promise in clinical trials, although they are ineffective against other members of the Ebolavirus genus that also cause periodic, lethal outbreaks. In this study, we present a crystal structure of a pan-ebolavirus antibody, 6D6, as well as single-particle electron microscopy reconstructions of 6D6 in complex with Ebola and Bundibugyo virus glycoproteins. 6D6 binds to the conserved glycoprotein fusion peptide, implicating it as a site of immune vulnerability that could be exploited to reliably elicit a pan-ebolavirus neutralizing antibody response.
History
DepositionMay 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6D6 Fab heavy chain
B: 6D6 Fab light chain
C: 6D6 Fab heavy chain
D: 6D6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)96,7564
Polymers96,7564
Non-polymers00
Water6,071337
1
A: 6D6 Fab heavy chain
B: 6D6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,3782
Polymers48,3782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-23 kcal/mol
Surface area20280 Å2
MethodPISA
2
C: 6D6 Fab heavy chain
D: 6D6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,3782
Polymers48,3782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-23 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.226, 72.038, 107.149
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 6D6 Fab heavy chain


Mass: 24706.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody 6D6 Fab light chain


Mass: 23671.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 0.1 M Tris pH 7.6, 25% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→72.04 Å / Num. obs: 70193 / % possible obs: 94.2 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.6
Reflection shellResolution: 1.96→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.49 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i9r
Resolution: 1.96→68.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.82
RfactorNum. reflection% reflection
Rfree0.2349 1959 2.81 %
Rwork0.191 --
obs0.1922 69694 93.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→68.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 0 337 6846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076675
X-RAY DIFFRACTIONf_angle_d0.939092
X-RAY DIFFRACTIONf_dihedral_angle_d4.5823938
X-RAY DIFFRACTIONf_chiral_restr0.0591025
X-RAY DIFFRACTIONf_plane_restr0.0061147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0090.29591550.30045100X-RAY DIFFRACTION99
2.009-2.06330.32931360.28475131X-RAY DIFFRACTION100
2.0633-2.12410.3041000.26243247X-RAY DIFFRACTION63
2.1241-2.19260.26551650.25145135X-RAY DIFFRACTION99
2.1926-2.2710.45041080.34914004X-RAY DIFFRACTION78
2.271-2.36190.34291450.25745037X-RAY DIFFRACTION98
2.3619-2.46940.28811470.23415134X-RAY DIFFRACTION100
2.4694-2.59960.2651460.23315161X-RAY DIFFRACTION100
2.5996-2.76250.28851320.22444805X-RAY DIFFRACTION93
2.7625-2.97580.25991570.21365167X-RAY DIFFRACTION100
2.9758-3.27530.2481500.20385126X-RAY DIFFRACTION99
3.2753-3.74920.21441300.1794467X-RAY DIFFRACTION86
3.7492-4.72340.18321370.14074976X-RAY DIFFRACTION95
4.7234-68.12070.191510.14985245X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.36833.2506-3.99483.6791-3.47155.782-0.1831-0.4377-0.348-0.0287-0.2411-0.41630.36430.35920.53280.34390.03690.07010.3414-0.00190.413415.564-12.543-20.5085
24.45260.42080.38283.48382.40983.9193-0.10780.27580.3477-0.48650.08870.1998-0.2927-0.1152-0.01160.2289-0.019-0.00220.25790.02440.20572.4645-9.0417-21.2241
36.02442.9536-1.70511.6855-1.06573.1127-0.25260.14660.1321-0.17660.16060.13070.2002-0.0209-0.05880.27270.0254-0.01460.30860.0090.318910.4428-11.1998-26.5191
43.93191.74040.56622.0048-0.0350.39430.1519-0.20570.21170.1849-0.0774-0.0851-0.09050.0629-0.0260.2623-0.00650.04250.2799-0.07760.265819.4396-0.9006-12.8704
52.54961.70611.63241.80950.69395.7301-0.31360.152-0.0487-0.0077-0.15230.17480.2405-0.03040.59190.31270.01040.03730.3034-0.08960.362234.82284.9085-8.9687
63.1195-0.9702-0.09152.79420.72654.4812-0.1619-0.1122-0.05990.13460.0892-0.0524-0.3338-0.31710.15680.27510.00190.02050.2598-0.03820.336532.10588.8151-6.4049
74.23190.59852.20092.77281.75738.2624-0.06320.16210.00440.38550.1065-0.35060.25220.5829-0.11320.35610.054-0.01110.3721-0.05430.447642.26983.894-6.3051
84.43180.72182.60843.42592.09063.27440.1231-0.5450.84090.0828-0.42540.5969-0.2083-0.34420.23540.3582-0.08630.09830.53-0.15150.6478-2.81627.1013-4.4985
91.98572.0171.47743.22931.85531.57630.2204-0.44830.23770.4357-0.29520.32470.1474-0.28390.04560.3086-0.04930.08640.4328-0.10920.3711.66090.4899-2.5094
104.22810.3443-2.51024.57870.50264.32980.03270.31870.3886-0.54340.1287-0.2318-0.2085-0.0505-0.16320.2828-0.03620.00490.2597-0.00230.318130.378521.6257-9.2206
111.7634-1.46970.57843.039-0.66871.9050.111-0.02890.0085-0.09220.0075-0.04590.2465-0.2627-0.18770.2766-0.0613-0.02170.3147-0.00880.2744-32.2847-12.3713-28.358
125.2881-0.68081.29223.41140.96683.6080.10010.08650.35910.12160.0059-0.0995-0.20370.2366-0.09770.2727-0.03030.02130.2412-0.01820.283-20.3024-12.0419-27.727
132.5709-0.50011.52141.5986-0.40572.1056-0.0350.2005-0.10990.10330.01910.193-0.04960.08360.06030.2612-0.00340.00560.2223-0.02840.197-32.9752-13.2668-38.7841
142.83950.1548-0.33536.60222.21164.4095-0.1980.1069-0.64610.4236-0.14830.95020.7355-0.52490.24310.4749-0.0880.06910.389-0.05730.6554-51.4219-17.8105-50.5273
153.2644-0.6919-0.64833.47460.4482.08850.35110.7155-0.0878-0.9173-0.2517-0.3563-0.16860.3278-0.0470.59360.11630.0930.7377-0.02360.4477-17.1122-25.4108-53.0514
161.9402-1.5109-2.48485.39060.05284.57960.1020.5980.206-0.06620.3145-0.5723-0.22591.4532-0.35020.4383-0.03250.06510.6718-0.08380.457-6.8564-23.1794-45.1074
174.0651-0.8818-0.44683.82041.98125.91640.06390.412-0.3736-0.1684-0.0275-0.02130.43910.3475-0.08630.36930.05-0.02510.3998-0.08080.2735-16.462-27.6136-41.6613
181.54970.45261.75950.13730.50222.11190.19460.0702-0.1434-0.31610.0703-0.1387-0.01320.3724-0.22210.590.12930.01610.43-0.05460.3649-29.1683-27.9275-60.774
193.667-2.3575-1.16148.09712.74275.366-0.03510.41650.0555-0.4457-0.34931.815-0.4006-1.21520.50840.58950.1539-0.16690.4672-0.21660.8782-54.353-10.1169-61.2824
205.3029-3.4524-0.77177.1231.57833.67860.45110.56630.1904-0.8625-0.49320.1432-0.51230.22020.13330.4893-0.0218-0.03470.38360.00230.3174-40.2535-14.9353-64.8523
214.0941-1.84-0.35966.5631.34554.7784-0.08490.1880.0357-0.31540.0376-0.016-0.24780.29580.01420.4155-0.0598-0.01070.4451-0.02420.4212-38.4193-16.0849-61.2629
222.41710.39490.70322.2829-1.78291.88710.61680.86150.0632-1.4186-0.86210.3488-0.8876-0.60120.13080.90120.3383-0.17190.5733-0.08530.425-46.078-9.648-69.4876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 162 )
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 193 )
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 219 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 32 )
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 114 )
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 213 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 25 )
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 83 )
13X-RAY DIFFRACTION13chain 'C' and (resid 84 through 142 )
14X-RAY DIFFRACTION14chain 'C' and (resid 143 through 219 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 18 )
16X-RAY DIFFRACTION16chain 'D' and (resid 19 through 32 )
17X-RAY DIFFRACTION17chain 'D' and (resid 33 through 102 )
18X-RAY DIFFRACTION18chain 'D' and (resid 103 through 114 )
19X-RAY DIFFRACTION19chain 'D' and (resid 115 through 129 )
20X-RAY DIFFRACTION20chain 'D' and (resid 130 through 151 )
21X-RAY DIFFRACTION21chain 'D' and (resid 152 through 175 )
22X-RAY DIFFRACTION22chain 'D' and (resid 176 through 212 )

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