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- PDB-6yor: Structure of the SARS-CoV-2 spike S1 protein in complex with CR30... -

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Basic information

Entry
Database: PDB / ID: 6yor
TitleStructure of the SARS-CoV-2 spike S1 protein in complex with CR3022 Fab
Components
  • IgG H chain
  • IgG L chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 Spike protein / RBD / CR3022 / complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell surface receptor binding / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane
Spike glycoprotein S2, coronavirus / Spike receptor binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike receptor binding domain superfamily, coronavirus
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHuo, J. / Zhao, Y. / Ren, J. / Zhou, D. / Duyvesteyn, H.M.E. / Carrique, L. / Malinauskas, T. / Ruza, R.R. / Shah, P.N.M. / Fry, E.E. / Owens, R. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: Cell Host Microbe / Year: 2020
Title: Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.
Authors: Jiandong Huo / Yuguang Zhao / Jingshan Ren / Daming Zhou / Helen M E Duyvesteyn / Helen M Ginn / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila ...Authors: Jiandong Huo / Yuguang Zhao / Jingshan Ren / Daming Zhou / Helen M E Duyvesteyn / Helen M Ginn / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Naomi Coombes / Kevin R Bewley / Julia A Tree / Julika Radecke / Neil G Paterson / Piyasa Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles Carroll / Alain Townsend / Elizabeth E Fry / Raymond J Owens / David I Stuart /
Abstract: There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes ...There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2, initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralizing SARS-CoV-2, and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilizing CR3022 epitope is inaccessible in the prefusion spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryogenic electron microscopy (cryo-EM) analysis confirms that incubation of spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope could be useful therapeutically, possibly in synergy with an antibody that blocks receptor attachment.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2May 13, 2020Group: Source and taxonomy / Category: em_entity_assembly_naturalsource / Item: _em_entity_assembly_naturalsource.organism

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
E: Spike glycoprotein
H: IgG H chain
L: IgG L chain
A: Spike glycoprotein
B: IgG H chain
C: IgG L chain


Theoretical massNumber of molelcules
Total (without water)143,0086
Polymers143,0086
Non-polymers00
Water0
1
E: Spike glycoprotein
H: IgG H chain
L: IgG L chain


Theoretical massNumber of molelcules
Total (without water)71,5043
Polymers71,5043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
A: Spike glycoprotein
B: IgG H chain
C: IgG L chain


Theoretical massNumber of molelcules
Total (without water)71,5043
Polymers71,5043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 22758.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Protein IgG H chain


Mass: 24455.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody IgG L chain


Mass: 24289.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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
IDNameTypeEntity IDParent-IDSource
1Binary complex of SARS-CoV-2 spike S1 with CR3022 FabCOMPLEX1, 2, 30RECOMBINANT
2RBDCOMPLEX11RECOMBINANT
3Immunoblobulin heavy chainCOMPLEX21RECOMBINANT
4Immunoblobulin light chainCOMPLEX31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Severe acute respiratory syndrome coronavirus 22697049
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Buffer solutionpH: 8 / Details: 2 mM Tris pH 8.0, 200 mM NaCl, 0.02 % NaN3
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13307

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategoryDetailsImage processing-ID
1cryoSPARC2.14.1-liveparticle selectionBlob picker module was initially used and templates were generated from this to then use Template Picker-driven particle picking.1
4Gctf1.06CTF correction1
10cryoSPARC2.14.1-liveinitial Euler assignment1
112.14.1-livefinal Euler assignment1
12cryoSPARC2.14.1-liveclassification1
13RELION3.13D reconstruction1
14cryoSPARC2.14.1-liveparticle selection2
22GctfCTF correction2
23cryoSPARC2.14.1-liveinitial Euler assignment2
24cryoSPARC2.14.1-livefinal Euler assignment2
25cryoSPARC2.14.1-liveclassification2
26cryoSPARC2.14.1-live3D reconstruction2
Image processing
IDImage recording-ID
11
21
CTF correction
IDDetailsImage processing-IDType
1Default settings in Gctf.1PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
IDImage processing-IDNum. of particles selectedDetails
114852523Initial from template generated with subset of data.
224852523
Symmetry
IDImage processing-IDEntry-IDPoint symmetry
116YORC1 (asymmetric)
226YORC1 (asymmetric)
3D reconstruction

Algorithm: BACK PROJECTION / Entry-ID: 6YOR / Num. of class averages: 1 / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT

IDResolution (Å)Num. of particlesImage processing-ID
13.33279451
23.91002952
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029956
ELECTRON MICROSCOPYf_angle_d0.51513542
ELECTRON MICROSCOPYf_dihedral_angle_d17.1643554
ELECTRON MICROSCOPYf_chiral_restr0.0441490
ELECTRON MICROSCOPYf_plane_restr0.0041734

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