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- PDB-7kfg: Antibody Fab BDBV-289 -

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Basic information

Entry
Database: PDB / ID: 7kfg
TitleAntibody Fab BDBV-289
Components
  • Antibody Fab BDBV-289 heavy chain
  • Antibody Fab BDBV-289 light chain
KeywordsIMMUNE SYSTEM / ebolavirus / antibody / broadly neutralizing / glycan cap / VIRAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsMurin, C.D. / Bruhn, J.F. / Ward, A.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109762 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2021
Title: Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies.
Authors: Charles D Murin / Pavlo Gilchuk / Philipp A Ilinykh / Kai Huang / Natalia Kuzmina / Xiaoli Shen / Jessica F Bruhn / Aubrey L Bryan / Edgar Davidson / Benjamin J Doranz / Lauren E Williamson ...Authors: Charles D Murin / Pavlo Gilchuk / Philipp A Ilinykh / Kai Huang / Natalia Kuzmina / Xiaoli Shen / Jessica F Bruhn / Aubrey L Bryan / Edgar Davidson / Benjamin J Doranz / Lauren E Williamson / Jeffrey Copps / Tanwee Alkutkar / Andrew I Flyak / Alexander Bukreyev / James E Crowe / Andrew B Ward /
Abstract: Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of ...Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1-69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies.
History
DepositionOct 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Fab BDBV-289 heavy chain
B: Antibody Fab BDBV-289 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7213
Polymers47,6152
Non-polymers1061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-22 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.460, 94.460, 94.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Antibody Antibody Fab BDBV-289 heavy chain


Mass: 24704.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Homo sapiens (human)
#2: Antibody Antibody Fab BDBV-289 light chain


Mass: 22910.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
Has ligand of interestN
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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M HEPES pH 6.5 and 20% (w/v) polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9473 / % possible obs: 97.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 68.35 Å2 / Rpim(I) all: 0.083 / Rrim(I) all: 0.19 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.5 % / Rpim(I) all: 0.612 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swiss model

Resolution: 3.002→37.563 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 927 9.78 %
Rwork0.2214 --
obs0.2259 9473 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.002→37.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 7 0 3270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023348
X-RAY DIFFRACTIONf_angle_d0.5124560
X-RAY DIFFRACTIONf_dihedral_angle_d14.5671200
X-RAY DIFFRACTIONf_chiral_restr0.046515
X-RAY DIFFRACTIONf_plane_restr0.003586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.002-3.16020.33531400.32731216X-RAY DIFFRACTION97
3.1602-3.35810.32321350.28361204X-RAY DIFFRACTION98
3.3581-3.61710.32761360.25211213X-RAY DIFFRACTION98
3.6171-3.98080.3131340.24831222X-RAY DIFFRACTION98
3.9808-4.5560.25221250.19411220X-RAY DIFFRACTION98
4.556-5.73670.20511260.19361244X-RAY DIFFRACTION99
5.7367-37.560.24351310.19021229X-RAY DIFFRACTION96
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)
14.3603-1.3234-1.82915.9095-1.13245.28790.0453-0.0345-0.16620.1084-0.4414-0.7211-0.52680.80440.0180.4063-0.01090.01220.47050.02820.3382-24.0937-17.4487-9.8916
25.7152-1.6168-1.08953.95270.02494.28710.67621.51610.3306-1.0484-0.46210.8823-0.0685-1.5913-0.03320.79430.3282-0.23291.0583-0.27030.7811-41.53-50.64262.9867
35.12950.3553-1.94653.5782-0.03385.96750.8705-0.3840.48810.8119-0.23760.1044-1.39910.0692-0.12391.13760.1870.24850.41680.04360.4699-37.7645-9.76942.9432
45.9629-5.51880.0968.6688-2.52447.9810.3677-0.27370.2670.30770.3139-0.3114-0.26120.6243-0.44670.44470.0389-0.00820.54550.00140.7233-38.5822-42.656317.187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 229 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 109 )
4X-RAY DIFFRACTION4chain 'B' and (resid 110 through 211 )

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