[English] 日本語
Yorodumi
- EMDB-66901: SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 Z... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66901
TitleSARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 ZL58 Fabs and 3 ZL525 Fabs, focused refinement of RBD and Fab region
Map data
Sample
  • Complex: SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 ZL58 Fabs and 3 ZL525 Fabs, focused refinement of RBD and Fab region
    • Protein or peptide: Heavy chain of ZL525 Fab
    • Protein or peptide: Light chain of ZL525 Fab
    • Protein or peptide: Heavy chain of ZL58 Fab
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Light chain of ZL58 Fab
KeywordsSpike protein / Antibody Fab fragment / Complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsNiu C / Liu B / Gao X / Li Z / He J / Xiong X
Funding support China, 8 items
OrganizationGrant numberCountry
Other government2021YFA1300903
National Natural Science Foundation of China (NSFC)82341085 China
Other governmentEKPG21-06
Other governmentSRPG22-002
Other government2021A1515011289
Other government2023B1212060050
Other government2023B1212120009
Other governmentGIBHBRP24-02
CitationJournal: To Be Published
Title: AI identifies Elite Antibodies that Tolerate Escape Mutations from a Population Antibody Class Exerting Continued Selection Over SARS-CoV-2
Authors: Niu C / Huang X / Yan Q / Liu B / Gao X / Song Y / Wang J / Wang L / Li Z / Zheng H / He P / Huang X / Yuan H / Zou B / Yang Y / Wu F / Yao Y / Chen X / Chen L / He J / Yao J / Zhao J / Xiong X
History
DepositionNov 2, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66901.png

Downloads & links

-
Map

FileDownload / File: emd_66901.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 360 pix.
= 373.76 Å		1.04 Å/pix.
x 360 pix.
= 373.76 Å		1.04 Å/pix.
x 360 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.714922 - 2.5300741
Average (Standard dev.)0.0013788423 (±0.036453977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 373.75998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_66901_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66901_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 Z...

EntireName: SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 ZL58 Fabs and 3 ZL525 Fabs, focused refinement of RBD and Fab region
Components
  • Complex: SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 ZL58 Fabs and 3 ZL525 Fabs, focused refinement of RBD and Fab region
    • Protein or peptide: Heavy chain of ZL525 Fab
    • Protein or peptide: Light chain of ZL525 Fab
    • Protein or peptide: Heavy chain of ZL58 Fab
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Light chain of ZL58 Fab

-
Supramolecule #1: SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 Z...

SupramoleculeName: SARS-CoV-2 Omicron LP.8.1 spike trimer (S-6P) in complex with 3 ZL58 Fabs and 3 ZL525 Fabs, focused refinement of RBD and Fab region
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

-
Macromolecule #1: Heavy chain of ZL525 Fab

MacromoleculeName: Heavy chain of ZL525 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.189076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSMKV SCQASGGTFS SHPISWIRQA PGQGLEWMGR IIPIAGMTDY GQKFQGRITI TADTSTSTSY VELRGLRSQ DTAFYYCAKD VGYSDYGSAY YFHTWGQGTL ITVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VKKPGSSMKV SCQASGGTFS SHPISWIRQA PGQGLEWMGR IIPIAGMTDY GQKFQGRITI TADTSTSTSY VELRGLRSQ DTAFYYCAKD VGYSDYGSAY YFHTWGQGTL ITVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD

-
Macromolecule #2: Light chain of ZL525 Fab

MacromoleculeName: Light chain of ZL525 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.890318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SGAPGQRVTI SCTGSNSNIG AGYDVHWYQQ LPGTAPKLLI YRNNKRPSGV PDRFSGSKSD TSASLAITGL QAEDEAHYY CQSFDSSLGG SLFGGGTKLA VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSVLTQPPSV SGAPGQRVTI SCTGSNSNIG AGYDVHWYQQ LPGTAPKLLI YRNNKRPSGV PDRFSGSKSD TSASLAITGL QAEDEAHYY CQSFDSSLGG SLFGGGTKLA VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

-
Macromolecule #3: Heavy chain of ZL58 Fab

MacromoleculeName: Heavy chain of ZL58 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.32902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLELVQSGGG LVQPGGSLRL SCAASEIAVS RNYMNWVRQG PGKGLEWVSI IYPGGSTFYA DSVKGRFTIS TDDSKNTLYL QMDSLSTDD TALYYCARQG PNGRNDFWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
QLELVQSGGG LVQPGGSLRL SCAASEIAVS RNYMNWVRQG PGKGLEWVSI IYPGGSTFYA DSVKGRFTIS TDDSKNTLYL QMDSLSTDD TALYYCARQG PNGRNDFWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

-
Macromolecule #4: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.062898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VTNLCPFHEV FNATTFASVY AWNRTRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IKGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKRSGNYD YWYRSLRKSK LKPFERDIST EIYQAGNKPC KGKGPNCYFP L ESYGFRPT ...String:
VTNLCPFHEV FNATTFASVY AWNRTRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IKGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKRSGNYD YWYRSLRKSK LKPFERDIST EIYQAGNKPC KGKGPNCYFP L ESYGFRPT YGVGHQPYRV VVLSFELLHA PATVCGP

UniProtKB: Spike glycoprotein

-
Macromolecule #5: Light chain of ZL58 Fab

MacromoleculeName: Light chain of ZL58 Fab / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.466951 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASAGERVT ITCQASQDIN MYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSVTE FTFTISSLQP EDIGTYYCH QYDSFPPTFG GGTKVDLKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASAGERVT ITCQASQDIN MYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSVTE FTFTISSLQP EDIGTYYCH QYDSFPPTFG GGTKVDLKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (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: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8wxl

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 237455
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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