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- PDB-6nb6: SARS-CoV complex with human neutralizing S230 antibody Fab fragme... -

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Basic information

Entry
Database: PDB / ID: 6nb6
TitleSARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 1)
Components
  • S230 heavy chain
  • S230 light chain
  • Spike glycoprotein
KeywordsVIRUS / coronavirus spike glycoprotein / MERS-CoV / SARS-CoV / human neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyCoronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell ...Coronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding / Spike glycoprotein
Function and homology information
Specimen sourceSARS coronavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsWalls, A.C. / Xiong, X. / Park, Y.J. / Tortorici, M.A. / Snijder, S. / Quispe, J. / Cameroni, E. / Gopal, R. / Mian, D. / Lanzavecchia, A. / Zambon, M. / Rey, F.A. / Corti, D. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Cell / Year: 2019
Title: Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.
Authors: Alexandra C Walls / Xiaoli Xiong / Young-Jun Park / M Alejandra Tortorici / Joost Snijder / Joel Quispe / Elisabetta Cameroni / Robin Gopal / Mian Dai / Antonio Lanzavecchia / Maria Zambon / Félix A Rey / Davide Corti / David Veesler
Abstract: Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways ...Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 6, 2018 / Release: Feb 6, 2019

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Structure visualization

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
H: S230 heavy chain
I: S230 heavy chain
L: S230 light chain
M: S230 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)503,398156
Polyers472,7377
Non-polymers30,661149
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 3 types, 7 molecules ABCHILM

#1: Protein/peptide Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 139815.969 Da / Num. of mol.: 3 / Source: (gene. exp.) SARS coronavirus / Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P59594
#2: Protein/peptide S230 heavy chain


Mass: 14314.899 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide S230 light chain


Mass: 12329.663 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 149 molecules

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


Mass: 221.208 Da / Num. of mol.: 93 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical...
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 37 / Formula: C6H12O6
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 19 / Formula: C6H12O6

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: SARS-CoV S complex with human neutralizing S230 antibody Fab fragment (state 1)
Type: COMPLEX / Entity ID: 1,2,3 / Source: RECOMBINANT
Molecular weightValue: 572 MDa / Experimental value: YES
Source (natural)Organism: SARS coronavirus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginon3.2image acquisition
7UCSF Chimeramodel fitting
9Rosettamodel refinement
11RELION3.0final Euler assignment
13RELION3.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 23071 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL

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