[English] 日本語
Yorodumi
- EMDB-11184: Association of two complexes of largely structurally disordered S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11184
TitleAssociation of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab
Map data
SampleComplex of SARS-CoV-2 Spike ectodomain with EY6A Fab
  • SARS-CoV-2 neutralizing antibody EY6A Fab
  • Spike glycoproteinPeplomer
  • EY6A heavy chain
  • EY6A light chain
  • ligand
Function / homology
Function and homology information


suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / 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 (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike glycoprotein S2, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2 / human (human) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsDuyvesteyn HME / Zhou D / Zhao Y / Fry EE / Ren J / Stuart DI
Funding support United Kingdom, China, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 China
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.
Authors: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / ...Authors: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / Che Ma / Jiandong Huo / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Robert F Donat / Kerry Godwin / Karen R Buttigieg / Julia A Tree / Julika Radecke / Neil G Paterson / Piyada Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles W Carroll / Javier Gilbert-Jaramillo / Michael L Knight / William James / Raymond J Owens / James H Naismith / Alain R Townsend / Elizabeth E Fry / Yuguang Zhao / Jingshan Ren / David I Stuart / Kuan-Ying A Huang /
Abstract: The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID- ...The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (K of 2 nM), and a 2.6-Å-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 17, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zfo
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zfo
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_11184.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 560 pix.
= 464.8 Å
0.83 Å/pix.
x 560 pix.
= 464.8 Å
0.83 Å/pix.
x 560 pix.
= 464.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.22 / Movie #1: 0.22
Minimum - Maximum-1.9675707 - 2.5311444
Average (Standard dev.)0.0010336173 (±0.022163555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 464.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z464.800464.800464.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-1.9682.5310.001

-
Supplemental data

-
Sample components

+
Entire Complex of SARS-CoV-2 Spike ectodomain with EY6A Fab

EntireName: Complex of SARS-CoV-2 Spike ectodomain with EY6A Fab
Details: SDS PAGE analysis shows that the Spike polypeptide remains largely uncleaved, while the density only shows S1 subunit
Number of components: 6

+
Component #1: protein, Complex of SARS-CoV-2 Spike ectodomain with EY6A Fab

ProteinName: Complex of SARS-CoV-2 Spike ectodomain with EY6A Fab
Details: SDS PAGE analysis shows that the Spike polypeptide remains largely uncleaved, while the density only shows S1 subunit
Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

+
Component #2: protein, SARS-CoV-2 neutralizing antibody EY6A Fab

ProteinName: SARS-CoV-2 neutralizing antibody EY6A Fab / Recombinant expression: No
SourceSpecies: human (human)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

+
Component #3: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.776381 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

+
Component #4: protein, EY6A heavy chain

ProteinName: EY6A heavy chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.346273 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

+
Component #5: protein, EY6A light chain

ProteinName: EY6A light chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.315855 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

+
Component #6: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: OTHER

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42.2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 119343
3D reconstructionSoftware: cryoSPARC / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more