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- PDB-5fhb: Crystal Structure of Protective Ebola Virus Antibody 100 -

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Basic information

Entry
Database: PDB / ID: 5fhb
TitleCrystal Structure of Protective Ebola Virus Antibody 100
Components
  • Antibody 100 Fab heavy chain
  • Antibody 100 Fab light chain
KeywordsIMMUNE SYSTEM / Ig domain / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
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 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._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 100 Fab heavy chain
L: Antibody 100 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,46114
Polymers46,7222
Non-polymers73912
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint8 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.540, 71.540, 199.012
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-485-

HOH

21L-562-

HOH

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Components

#1: Antibody Antibody 100 Fab heavy chain


Mass: 24337.166 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 100 Fab light chain


Mass: 22384.715 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3.4mg/ml 100 Fab, 38% PEG 400, 4.75% PEG 3350, 0.1M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.97→33.487 Å / Num. obs: 42605 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 24.01 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.044 / Net I/σ(I): 11.3 / Num. measured all: 443933 / Scaling rejects: 587
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.97-2.029.10.7513.12679229330.860.261100
9.04-38.798.50.04318.543985170.9980.01597.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
MOSFLMdata reduction
Aimless0.5.15data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 4QHK

4qhk


Resolution: 1.973→33.487 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 2016 4.74 %
Rwork0.1586 --
obs0.1602 42508 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→33.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 48 291 3625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183412
X-RAY DIFFRACTIONf_angle_d1.6234645
X-RAY DIFFRACTIONf_dihedral_angle_d15.0461216
X-RAY DIFFRACTIONf_chiral_restr0.102525
X-RAY DIFFRACTIONf_plane_restr0.008588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.973-2.02240.25651400.21362838X-RAY DIFFRACTION100
2.0224-2.0770.23191640.18822821X-RAY DIFFRACTION100
2.077-2.13810.20021420.16132831X-RAY DIFFRACTION100
2.1381-2.20710.18661540.15882828X-RAY DIFFRACTION100
2.2071-2.2860.19981430.15382858X-RAY DIFFRACTION100
2.286-2.37750.19991640.1612860X-RAY DIFFRACTION100
2.3775-2.48570.21291480.15552855X-RAY DIFFRACTION100
2.4857-2.61670.19311480.15252837X-RAY DIFFRACTION100
2.6167-2.78060.20341380.15292906X-RAY DIFFRACTION100
2.7806-2.99510.19141410.14662898X-RAY DIFFRACTION100
2.9951-3.29630.18341370.15072889X-RAY DIFFRACTION100
3.2963-3.77270.19241540.14952942X-RAY DIFFRACTION100
3.7727-4.75110.16741160.14552990X-RAY DIFFRACTION100
4.7511-33.49210.1931270.18153139X-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)
12.51050.91690.75962.1911-0.33342.63350.1332-0.0082-0.34930.12530.0286-0.13880.3797-0.0136-0.12340.2556-0.032-0.01870.1132-0.00350.184821.8297-31.501532.9313
22.0033-0.0566-1.16051.1271-0.38763.2776-0.0220.08150.10180.0215-0.0014-0.2665-0.02330.1530.02530.2521-0.1001-0.00310.15120.01840.210527.4773-21.13482.9401
31.5270.62430.09582.6087-0.85672.6359-0.01570.03870.117-0.01290.0164-0.09230.03720.0261-0.01320.13790.005800.0715-0.00950.15333.7908-13.380236.4645
41.91391.80270.69143.95242.44642.87710.12280.0076-0.01420.1616-0.0094-0.09290.0855-0.0827-0.07940.2264-0.0539-0.01820.12510.00180.170324.5479-5.6172-0.0729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:107)
2X-RAY DIFFRACTION2(chain H and resid 108:215)
3X-RAY DIFFRACTION3(chain L and resid 2:109)
4X-RAY DIFFRACTION4(chain L and resid 110:209)

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