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- PDB-5fha: Crystal Structure of Protective Ebola Virus Antibody 114 -

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Basic information

Entry
Database: PDB / ID: 5fha
TitleCrystal Structure of Protective Ebola Virus Antibody 114
Components
  • Antibody 114 Fab heavy chain
  • Antibody 114 Fab light chain
KeywordsIMMUNE SYSTEM / Ig domain / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.973 Å
AuthorsGilman, M.S.A. / McLellan, J.S.
CitationJournal: Science / Year: 2016
Title: Structural and molecular basis for Ebola virus neutralization by protective human antibodies.
Authors: John Misasi / Morgan S A Gilman / Masaru Kanekiyo / Miao Gui / Alberto Cagigi / Sabue Mulangu / Davide Corti / Julie E Ledgerwood / Antonio Lanzavecchia / James Cunningham / Jean Jacques ...Authors: John Misasi / Morgan S A Gilman / Masaru Kanekiyo / Miao Gui / Alberto Cagigi / Sabue Mulangu / Davide Corti / Julie E Ledgerwood / Antonio Lanzavecchia / James Cunningham / Jean Jacques Muyembe-Tamfun / Ulrich Baxa / Barney S Graham / Ye Xiang / Nancy J Sullivan / Jason S McLellan /
Abstract: Ebola virus causes hemorrhagic fever with a high case fatality rate for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination, protect nonhuman ...Ebola virus causes hemorrhagic fever with a high case fatality rate for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination, protect nonhuman primates against all signs of Ebola virus disease, including viremia. Here, we demonstrate that mAb100 recognizes the base of the Ebola virus glycoprotein (GP) trimer, occludes access to the cathepsin-cleavage loop, and prevents the proteolytic cleavage of GP that is required for virus entry. We show that mAb114 interacts with the glycan cap and inner chalice of GP, remains associated after proteolytic removal of the glycan cap, and inhibits binding of cleaved GP to its receptor. These results define the basis of neutralization for two protective antibodies and may facilitate development of therapies and vaccines.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _atom_site.occupancy / _citation.journal_id_CSD ..._atom_site.occupancy / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Antibody 114 Fab heavy chain
L: Antibody 114 Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,1462
Polymers46,1462
Non-polymers00
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-21 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.540, 63.900, 39.130
Angle α, β, γ (deg.)90.00, 101.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-312-

HOH

21H-388-

HOH

31H-453-

HOH

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Components

#1: Antibody Antibody 114 Fab heavy chain


Mass: 23203.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: PBMC / Cell line (production host): HEK293 Cells / Production host: Homo sapiens (human)
#2: Antibody Antibody 114 Fab light chain


Mass: 22942.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: PBMC / Cell line (production host): HEK293 Cells / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5.29mg/mL 114 Fab, 27% PEG 3350, 4.32% isopropanol, 0.1M HEPES pH 7.5, 0.1M calcium chloride, 0.01M sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.97→42.12 Å / Num. obs: 29265 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.768 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.079 / Net I/σ(I): 7.4 / Num. measured all: 100911 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.97-2.0230.7872.1639821300.4220.55499.8
8.82-42.123.40.03915.211963550.9970.02498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8R, 3WD5

4k8r

3wd5


Resolution: 1.973→42.117 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1389 4.75 %
Rwork0.1792 --
obs0.1816 29263 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.973→42.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 0 333 3541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053281
X-RAY DIFFRACTIONf_angle_d0.914455
X-RAY DIFFRACTIONf_dihedral_angle_d11.9181169
X-RAY DIFFRACTIONf_chiral_restr0.033508
X-RAY DIFFRACTIONf_plane_restr0.004572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.973-2.04350.32231420.25432758X-RAY DIFFRACTION100
2.0435-2.12530.29681400.23422761X-RAY DIFFRACTION100
2.1253-2.22210.26881360.2122766X-RAY DIFFRACTION100
2.2221-2.33920.24621380.21452775X-RAY DIFFRACTION100
2.3392-2.48570.24461420.20032781X-RAY DIFFRACTION100
2.4857-2.67760.25431580.18252770X-RAY DIFFRACTION100
2.6776-2.9470.21851170.1752794X-RAY DIFFRACTION100
2.947-3.37330.21611490.15982791X-RAY DIFFRACTION100
3.3733-4.24940.20411400.14992795X-RAY DIFFRACTION100
4.2494-42.1270.19521270.16232883X-RAY DIFFRACTION100
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)
12.01580.7295-1.21431.67340.34661.7604-0.37390.3332-0.45880.16160.05110.00950.5729-0.20110.08040.2578-0.05090.07880.1539-0.03140.2228-9.5815-32.57586.3819
21.5853-0.8425-0.71351.30530.23961.8756-0.2378-0.1553-0.19490.12020.18660.27240.0264-0.31960.0380.06950.03640.03290.23770.05720.173-20.9756-14.635920.806
33.952-2.0269-2.92391.52551.67252.2676-0.0966-0.99520.18370.29920.1642-0.0203-0.527-0.4393-0.02050.25670.20410.02120.4965-0.06980.1314-15.702-6.941329.7575
41.75240.25210.66620.97280.621.0469-0.13391.5103-0.0245-0.9266-0.1340.28220.0203-0.89010.32760.0782-0.3693-0.11540.8347-0.19980.3234-33.5777-31.2172.2861
51.2781-0.129-0.65760.90270.26150.52-0.47611.165-0.53450.11980.04220.63510.6511-0.7820.08460.2418-0.34750.07560.4676-0.27140.4747-33.7532-34.37056.0521
63.73130.58940.18283.53260.68011.92540.02-0.1010.1632-0.1588-0.06580.011-0.2506-0.16870.00020.12960.07030.00450.16010.02560.1379-33.0253-0.229417.2561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:85)
2X-RAY DIFFRACTION2(chain H and resid 86:198)
3X-RAY DIFFRACTION3(chain H and resid 199:214)
4X-RAY DIFFRACTION4(chain L and resid 1:43)
5X-RAY DIFFRACTION5(chain L and resid 44:107)
6X-RAY DIFFRACTION6(chain L and resid 108:212)

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