[English] 日本語
Yorodumi
- EMDB-39806: Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39806
TitleStructure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
Map dataSome local resolutions of the map are low, and the local structure is built based on the high-resolution local map (EMD-39807), and then fit into the overall map.
Sample
  • Complex: Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
    • Protein or peptide: Spike glycoprotein,Fibritin,Expression Tag
    • Protein or peptide: CYFN1006-2 light chain
    • Protein or peptide: CYFN1006-2 heavy chain
Keywordsantibody / viral protein / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


virion component / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion ...virion component / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsWang YJ / Sun L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
Authors: Wang YJ / Sun L
History
DepositionApr 19, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_39806.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSome local resolutions of the map are low, and the local structure is built based on the high-resolution local map (EMD-39807), and then fit into the overall map.
Voxel sizeX=Y=Z: 1.19 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.7278591 - 2.2899556
Average (Standard dev.)0.0004403961 (±0.042146735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 571.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibo...

EntireName: Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
Components
  • Complex: Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
    • Protein or peptide: Spike glycoprotein,Fibritin,Expression Tag
    • Protein or peptide: CYFN1006-2 light chain
    • Protein or peptide: CYFN1006-2 heavy chain

-
Supramolecule #1: Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibo...

SupramoleculeName: Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron/EG.5.1

-
Macromolecule #1: Spike glycoprotein,Fibritin,Expression Tag

MacromoleculeName: Spike glycoprotein,Fibritin,Expression Tag / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 143.147594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTH DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PALPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS ...String:
MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTH DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PALPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS SANNCTFEYV SQPFLMDLEG KEGNFKNLRE FVFKNIDGYF KIYSKHTPIN LERDLPQGFS ALEPLVDLPI GI NITRFQT LLALHRSYLT PVDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIY QTSNFR VQPTESIVRF PNITNLCPFH EVFNATTFAS VYAWNRKRIS NCVADYSVIY NFAPFFAFKC YGVSPTKLND LCFT NVYAD SFVIRGNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKPSGN YNYLYRLLRK SKLKPFERDI STEIY QAGN KPCNGVAGPN CYSPLQSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLT ESN KKFLPFQQFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTW RV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIA I PTNFTISVTT EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTI TSGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV N HNAQALNT LVKQLSSKFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CV LGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQ IITTDN TFVSGNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNL NESLI DLQELGKYEQ GSGYIPEAPR DGQAYVRKDG EWVFLSTFLS GLEVLFQGPG GWSHPQFEKG GGSGGGSGGS AWSHP QFEK GGSHHHHHHH H

UniProtKB: Spike glycoprotein, Fibritin

-
Macromolecule #2: CYFN1006-2 light chain

MacromoleculeName: CYFN1006-2 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.673113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPPSA SGSPGQSVTI SCTGASSDVG GYNYVSWYQQ HPGKAPKLMI YEVNKRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYALSRVV FGGGTMLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS ...String:
QSALTQPPSA SGSPGQSVTI SCTGASSDVG GYNYVSWYQQ HPGKAPKLMI YEVNKRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYALSRVV FGGGTMLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

-
Macromolecule #3: CYFN1006-2 heavy chain

MacromoleculeName: CYFN1006-2 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.388381 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QMQLVQSGAE VKKPGESLKI SCKGSGYTFS YYWIGWVRQM PGKGLEWMGI IYPGDSDTRY SPSFQGQVTI SADKSISTAY LHWSSLKAS DTAMYYCARQ GDLGDWILLG YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QMQLVQSGAE VKKPGESLKI SCKGSGYTFS YYWIGWVRQM PGKGLEWMGI IYPGDSDTRY SPSFQGQVTI SADKSISTAY LHWSSLKAS DTAMYYCARQ GDLGDWILLG YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Predict the initial structure with SWISS
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 244940
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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