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- PDB-6pz8: MERS S0 trimer in complex with variable domain of antibody G2 -

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Basic information

Entry
Database: PDB / ID: 6pz8
TitleMERS S0 trimer in complex with variable domain of antibody G2
Components
  • (S protein) x 2
  • G2 heavy chain
  • G2 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / MERS-CoV / coronavirus / DPP4 / receptor-binding / membrane fusion / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion / receptor-mediated virion attachment to host cell / viral envelope / integral component of membrane
Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike receptor binding domain superfamily / Spike glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain
S protein / Spike glycoprotein
Biological speciesMiddle East respiratory syndrome-related coronavirus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsBowman, C.A. / Pallesen, J. / Ward, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI127521 United States
CitationJournal: Cell Rep / Year: 2019
Title: Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD.
Authors: Nianshuang Wang / Osnat Rosen / Lingshu Wang / Hannah L Turner / Laura J Stevens / Kizzmekia S Corbett / Charles A Bowman / Jesper Pallesen / Wei Shi / Yi Zhang / Kwanyee Leung / Robert N Kirchdoerfer / Michelle M Becker / Mark R Denison / James D Chappell / Andrew B Ward / Barney S Graham / Jason S McLellan /
Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the ...Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here, we report the structural and functional characterization of G2, a neutralizing antibody targeting the MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD define a site of vulnerability comprising two loops, each of which contain a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrate that G2 strongly disrupts the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4), with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate the development of immunotherapeutics and vaccines against MERS-CoV.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release

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Structure visualization

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  • EMDB-20527
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: S protein
B: S protein
H: G2 heavy chain
L: G2 light chain
E: S protein
J: S protein
C: G2 heavy chain
G: G2 light chain
I: S protein
F: S protein
D: G2 heavy chain
K: G2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)556,30390
Polymers539,54112
Non-polymers16,76278
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area55190 Å2
ΔGint64 kcal/mol
Surface area155470 Å2

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Components

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Protein/peptide , 4 types, 12 molecules AEIBJFHCDLGK

#1: Protein/peptide S protein


Mass: 51301.617 Da / Num. of mol.: 3 / Fragment: S2 C-terminal domain (UNP residues 753-1223)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Homo sapiens (human) / References: UniProt: W5ZZF5
#2: Protein/peptide S protein / Spike glycoprotein / Spike protein


Mass: 80409.109 Da / Num. of mol.: 3 / Fragment: S0 N-terminal domain (UNP residues 18-743)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Homo sapiens (human) / References: UniProt: W6A090
#3: Protein/peptide G2 heavy chain


Mass: 24275.059 Da / Num. of mol.: 3 / Fragment: variable domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Protein/peptide G2 light chain


Mass: 23861.293 Da / Num. of mol.: 3 / Fragment: variable domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 78 molecules

#5: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 66
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#7: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1MERS S0 ectodomain trimer in complex with antibody G21, 2, 3, 40MULTIPLE SOURCES
2MERS S0 ectodomain trimer1, 21RECOMBINANT
3antibody G23, 41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Middle East respiratory syndrome-related coronavirus1335626
23Mus musculus (house mouse)10090
Source (recombinant)

Ncbi tax-ID: 9606 / Organism: Homo sapiens (human)

IDEntity assembly-ID
12
23
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 77 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.13.1model fitting
10cryoSPARC2.5initial Euler assignment
11cryoSPARC2.5final Euler assignment
13cryoSPARC2.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 418781
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12386 / Symmetry type: POINT
Atomic model buildingDetails: Model was not refined.
Atomic model buildingPDB-ID: 5W9I

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