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- EMDB-39922: SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-39922
TitleSARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Map data
Sample
  • Complex: SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: Light chain of D1F6 Fab
    • Protein or peptide: Heavy chain of D1F6 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike protein / Antibody Fab fragment / Complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsLiu B / Gao X / Li Z / Chen Q / He J / Xiong X
Funding support3 items
OrganizationGrant numberCountry
Other governmentEKPG21-06
Other governmentSRPG22-002
Other government2021A1515011289
CitationJournal: To be published
Title: An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike
Authors: Liu B / Niu X / Deng Y / Zhang Z / Wang Y / Gao X / Liang H / Li Z / Wang Q / Cheng Y / Chen Q / Huang S / Pan Y / Su M / Lin X / Niu C / Chen Y / Yang W / Zhang Y / Yan Q / He J / Zhao J / Chen L / Xiong X
History
DepositionApr 28, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39922.png

Downloads & links

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Map

FileDownload / File: emd_39922.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.408 Å
Density
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-1.120859 - 1.6453243
Average (Standard dev.)0.00064390036 (±0.033779666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39922_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39922_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 ...

EntireName: SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Components
  • Complex: SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: Light chain of D1F6 Fab
    • Protein or peptide: Heavy chain of D1F6 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 ...

SupramoleculeName: SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron/BA.4
Molecular weightTheoretical: 137.621516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AISGTNGTKR FDNPVLPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF ...String:
QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AISGTNGTKR FDNPVLPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF KNLREFVFKN IDGYFKIYSK HTPINLGRDL PQGFSALEPL VDLPIGINIT RFQTLLALHR SYLTPGDSSS GW TAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPF DEVFNA TRFASVYAWN RKRISNCVAD YSVLYNFAPF FAFKCYGVSP TKLNDLCFTN VYADSFVIRG NEVSQIAPGQ TGNI ADYNY KLPDDFTGCV IAWNSNKLDS KVGGNYNYRY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGVNCYFPLQ SYGFR PTYG VGHQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLTGTGVL TESNKKFLPF QQFGRDIADT TDAVRD PQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVP VAIHADQLTP TWRVYSTGSN VFQTRAGCLI GAEYVNN SY ECDIPIGAGI CASYQTQTKS RSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISVTT EILPVSMTKT SVDCTMYI C GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAGP ALQIPFPMQM AYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQDV VNHNAQALNT LVKQLSSKFG AISSVLNDIL S RLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VF LHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFVSGNCDVV IGIVNNTVYD PLQ PELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIKGSGRENL YFQG GGGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGHHH HHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: Light chain of D1F6 Fab

MacromoleculeName: Light chain of D1F6 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.62327 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QPVLTQPPSA SGPPGQSVSI SCSGSRSNIG TNFVYWYQQL PGAAPKLLIY KNDQRPSGVP ERFFGSKSGT SASLAISGLR SEDEVDYYC AAWDDSLSGH VFGAGTKVTV LGTKLTVLGQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW K ADSSPVKA ...String:
QPVLTQPPSA SGPPGQSVSI SCSGSRSNIG TNFVYWYQQL PGAAPKLLIY KNDQRPSGVP ERFFGSKSGT SASLAISGLR SEDEVDYYC AAWDDSLSGH VFGAGTKVTV LGTKLTVLGQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW K ADSSPVKA GVETTTPSKQ SNNKYAASSY LSLTPEQWKS HRSYSCQVTH EGSTVEKTVA PTECS

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Macromolecule #3: Heavy chain of D1F6 Fab

MacromoleculeName: Heavy chain of D1F6 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.752727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKKPGASVKV SCKASGYIFS DYNIHWVRQA PGQGLEWMGW ISPDSDDTNY AQSFQGRVTM TRDTSITTVY MELSSLRSD DTAVYFCARS VGYCSLNSCQ RWMWFDTWGQ GALVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVQSGAE VKKPGASVKV SCKASGYIFS DYNIHWVRQA PGQGLEWMGW ISPDSDDTNY AQSFQGRVTM TRDTSITTVY MELSSLRSD DTAVYFCARS VGYCSLNSCQ RWMWFDTWGQ GALVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xnq

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 251455

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