[English] 日本語
Yorodumi
- EMDB-30523: S protein of SARS-CoV-2 in complex bound with FabP5A-1B8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30523
TitleS protein of SARS-CoV-2 in complex bound with FabP5A-1B8
Map data
SampleS protein of SARS-CoV-2 in complex bound with FabP5A-1B8
  • Spike glycoproteinPeplomer
  • IG c642_heavy_IGHV3-53_IGHD1-26_IGHJ6,chain H of FabP5A-1B8,IGH@ protein
  • IGL c4203_light_IGKV1-9_IGKJ4,Uncharacterized protein
  • 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 / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / viral protein processing / fusion of virus membrane with host plasma membrane ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / viral protein processing / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / viral entry into host cell / go:0009405: / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / membrane / integral component of membrane / identical protein binding
Spike glycoprotein S2, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Immunoglobulin-like fold / Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin C1-set ...Spike glycoprotein S2, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Immunoglobulin-like fold / Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Spike glycoprotein, betacoronavirus / Spike receptor binding domain superfamily, coronavirus / Immunoglobulin-like domain superfamily / Coronavirus spike glycoprotein S1, C-terminal / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2
IGL c4203_light_IGKV1-9_IGKJ4 / IG c642_heavy_IGHV3-53_IGHD1-26_IGHJ6 / Spike glycoprotein / IGH@ protein / Uncharacterized protein
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsYan RH / Zhang YY / Li YN / Zhou Q
CitationJournal: Cell Res / Year: 2021
Title: Structural basis for bivalent binding and inhibition of SARS-CoV-2 infection by human potent neutralizing antibodies.
Authors: Renhong Yan / Ruoke Wang / Bin Ju / Jinfang Yu / Yuanyuan Zhang / Nan Liu / Jia Wang / Qi Zhang / Peng Chen / Bing Zhou / Yaning Li / Yaping Shen / Shuyuan Zhang / Long Tian / Yingying Guo / ...Authors: Renhong Yan / Ruoke Wang / Bin Ju / Jinfang Yu / Yuanyuan Zhang / Nan Liu / Jia Wang / Qi Zhang / Peng Chen / Bing Zhou / Yaning Li / Yaping Shen / Shuyuan Zhang / Long Tian / Yingying Guo / Lu Xia / Xinyue Zhong / Lin Cheng / Xiangyang Ge / Juanjuan Zhao / Hong-Wei Wang / Xinquan Wang / Zheng Zhang / Linqi Zhang / Qiang Zhou /
Abstract: Neutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus disease 2019 ...Neutralizing monoclonal antibodies (nAbs) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent promising candidates for clinical intervention against coronavirus disease 2019 (COVID-19). We isolated a large number of nAbs from SARS-CoV-2-infected individuals capable of disrupting proper interaction between the receptor binding domain (RBD) of the viral spike (S) protein and the receptor angiotensin converting enzyme 2 (ACE2). However, the structural basis for their potent neutralizing activity remains unclear. Here, we report cryo-EM structures of the ten most potent nAbs in their native full-length IgG-form or in both IgG-form and Fab-form bound to the trimeric S protein of SARS-CoV-2. The bivalent binding of the full-length IgG is found to associate with more RBDs in the "up" conformation than the monovalent binding of Fab, perhaps contributing to the enhanced neutralizing activity of IgG and triggering more shedding of the S1 subunit from the S protein. Comparison of a large number of nAbs identified common and unique structural features associated with their potent neutralizing activities. This work provides a structural basis for further understanding the mechanism of nAbs, especially through revealing the bivalent binding and its correlation with more potent neutralization and the shedding of S1 subunit.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionSep 9, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7d00
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_30523.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 288 pix.
= 313.056 Å
1.09 Å/pix.
x 288 pix.
= 313.056 Å
1.09 Å/pix.
x 288 pix.
= 313.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.018
Minimum - Maximum-0.09549992 - 0.1921623
Average (Standard dev.)0.00023236607 (±0.0044591255)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 313.056 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z313.056313.056313.056
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0950.1920.000

-
Supplemental data

-
Sample components

+
Entire S protein of SARS-CoV-2 in complex bound with FabP5A-1B8

EntireName: S protein of SARS-CoV-2 in complex bound with FabP5A-1B8
Number of components: 5

+
Component #1: protein, S protein of SARS-CoV-2 in complex bound with FabP5A-1B8

ProteinName: S protein of SARS-CoV-2 in complex bound with FabP5A-1B8
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 142.502594 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

+
Component #3: protein, IG c642_heavy_IGHV3-53_IGHD1-26_IGHJ6,chain H of FabP5A-...

ProteinName: IG c642_heavy_IGHV3-53_IGHD1-26_IGHJ6,chain H of FabP5A-1B8,IGH@ protein
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 48.619664 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #4: protein, IGL c4203_light_IGKV1-9_IGKJ4,Uncharacterized protein

ProteinName: IGL c4203_light_IGKV1-9_IGKJ4,Uncharacterized protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.218801 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #5: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 28 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

-
Experimental details

-
Sample preparation

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

-
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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 239537
3D reconstructionSoftware: RELION / Resolution: 3 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