[English] 日本語
Yorodumi
- EMDB-28756: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28756
TitleStructure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3
Map data
Sample
  • Complex: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
    • Complex: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain
      • Protein or peptide: Antibody 1C3 Fab Heavy Chain
      • Protein or peptide: Antibody 1C3 Fab Light Chain
    • Complex: Spike glycoproteinSpike protein
      • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsYu X / Zyla D / Hastie KM / Saphire EO
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
GHR Foundation United States
CitationJournal: Cell Rep / Year: 2023
Title: Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.
Authors: Kathryn M Hastie / Xiaoying Yu / Fernanda Ana-Sosa-Batiz / Dawid S Zyla / Stephanie S Harkins / Chitra Hariharan / Hal Wasserman / Michelle A Zandonatti / Robyn Miller / Erin Maule / Kenneth ...Authors: Kathryn M Hastie / Xiaoying Yu / Fernanda Ana-Sosa-Batiz / Dawid S Zyla / Stephanie S Harkins / Chitra Hariharan / Hal Wasserman / Michelle A Zandonatti / Robyn Miller / Erin Maule / Kenneth Kim / Kristen M Valentine / Sujan Shresta / Erica Ollmann Saphire /
Abstract: Therapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly ...Therapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly emergent strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), particularly those of the Omicron lineage. Here, we report the identification of a panel of vaccinee-derived antibodies that have broad-spectrum neutralization activity. Structural and biochemical characterization of the three broadest-spectrum antibodies reveal complementary footprints and differing requirements for avidity to overcome variant-associated mutations in their binding footprints. In the K18 mouse model of infection, these three antibodies exhibit protective efficacy against BA.1 and BA.2 infection. This study highlights the resilience and vulnerabilities of SARS-CoV-2 antibodies and provides road maps for further development of broad-spectrum therapeutics.
History
DepositionNov 2, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28756.png

Downloads & links

-
Map

FileDownload / File: emd_28756.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.34171963 - 1.1367804
Average (Standard dev.)-0.00012936915 (±0.019845225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_28756_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28756_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibo...

EntireName: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
Components
  • Complex: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
    • Complex: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain
      • Protein or peptide: Antibody 1C3 Fab Heavy Chain
      • Protein or peptide: Antibody 1C3 Fab Light Chain
    • Complex: Spike glycoproteinSpike protein
      • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibo...

SupramoleculeName: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain

SupramoleculeName: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain
type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Spike glycoprotein

SupramoleculeName: Spike glycoprotein / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Macromolecule #1: Antibody 1C3 Fab Heavy Chain

MacromoleculeName: Antibody 1C3 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.718235 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLLESGGG LVQPGRSLRL SCAASGFTFD DYAMHWVRQP PGKGLEWVSG SSWNSGSVVY ADSVKGRFTI SRDSAKNSLH LQMNSLRVE DTALYYCAKA VDPTRGSYSP DYGFDIWGQG TMVTVSS

-
Macromolecule #2: Antibody 1C3 Fab Light Chain

MacromoleculeName: Antibody 1C3 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.554764 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DAIRMTQSPS SLSASVGDRV TITCRASQSI SSYLNWYQQK PGKAPNLLIY AASSLESGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYC QQSYSTPLTF GGGTKVEIK

-
Macromolecule #3: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 134.224359 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGVKVLFALI CIAVAEAQCV NLTTRTQLPP AYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH VISGTNGTKR FDNPVLPFN DGVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDHKNNK SWMESEFRVY S SANNCTFE ...String:
MGVKVLFALI CIAVAEAQCV NLTTRTQLPP AYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH VISGTNGTKR FDNPVLPFN DGVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDHKNNK SWMESEFRVY S SANNCTFE YVSQPFLMDL EGKQGNFKNL REFVFKNIDG YFKIYSKHTP IIVREPEDLP QGFSALEPLV DLPIGINITR FQ TLLALHR SYLTPGDSSS GWTAGAAAYY VGYLQPRTFL LKYNENGTIT DAVDCALDPL SETKCTLKSF TVEKGIYQTS NFR VQPTES IVRFPNITNL CPFDEVFNAT RFASVYAWNR KRISNCVADY SVLYNLAPFF TFKCYGVSPT KLNDLCFTNV YADS FVIRG DEVRQIAPGQ TGNIADYNYK LPDDFTGCVI AWNSNKLDSK VSGNYNYLYR LFRKSNLKPF ERDISTEIYQ AGNKP CNGV AGFNCYFPLR SYSFRPTYGV GHQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLKGTGVLT ESNKKF LPF QQFGRDIADT TDAVRDPQTL EILDITPCSF GGVSVITPGT NTSNQVAVLY QGVNCTEVPV AIHADQLTPT WRVYSTG SN VFQTRAGCLI GAEYVNNSYE CDIPIGAGIC ASYQTQTKSH GSASSVASQS IIAYTMSLGA ENSVAYSNNS IAIPTNFT I SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLKRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKYFGG FNFSQILPDP SKPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL ICAQKFKGLT VLPPLLTDEM IAQYTSALLA GTITSGWTF GAGPALQIPF PMQMAYRFNG IGVTQNVLYE NQKLIANQFN SAIGKIQDSL SSTPSALGKL QDVVNHNAQA L NTLVKQLS SKFGAISSVL NDIFSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KR VDFCGKG YHLMSFPQSA PHGVVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREGVFV SNGTHWFVTQ RNFYEPQIIT TDN TFVSGN CDVVIGIVNN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLID LQELG KYEQ

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: TBS buffer pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
Details: home-made GO grids with continues graphene oxide layer
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.1) / Number images used: 49958
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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. 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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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