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- EMDB-34655: SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB13-29... -

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Entry
Database: EMDB / ID: EMD-34655
TitleSARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB13-292 Fab, focused refinement of Fab region
Map dataFocused half map 2 of YB13-292 Fab complexed with Omicron S
Sample
  • Complex: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB13-292 Fab, focused refinement of Fab region
    • Complex: SARS-CoV-2 Omicron BA.1 spike protein
      • Protein or peptide: Spike protein S1
    • Complex: YB13-292 Fab
      • Protein or peptide: Heavy chain of YB13-292 Fab
      • Protein or peptide: Light chain of YB13-292 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike protein / RBD / antibody / Fab / Viral protein / 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 / viral translation / host extracellular space / 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 / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / 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
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 ...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
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsLiu B / Gao X / Chen Q / Li Z / Su M / He J / Xiong X
Funding support3 items
OrganizationGrant numberCountry
Other governmentEKPG21-06
Other government2021A1515011289
Other governmentGRMH-GL
CitationJournal: Nat Commun / Year: 2023
Title: Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Authors: Haisheng Yu / Banghui Liu / Yudi Zhang / Xijie Gao / Qian Wang / Haitao Xiang / Xiaofang Peng / Caixia Xie / Yaping Wang / Peiyu Hu / Jingrong Shi / Quan Shi / Pingqian Zheng / Chengqian ...Authors: Haisheng Yu / Banghui Liu / Yudi Zhang / Xijie Gao / Qian Wang / Haitao Xiang / Xiaofang Peng / Caixia Xie / Yaping Wang / Peiyu Hu / Jingrong Shi / Quan Shi / Pingqian Zheng / Chengqian Feng / Guofang Tang / Xiaopan Liu / Liliangzi Guo / Xiumei Lin / Jiaojiao Li / Chuanyu Liu / Yaling Huang / Naibo Yang / Qiuluan Chen / Zimu Li / Mengzhen Su / Qihong Yan / Rongjuan Pei / Xinwen Chen / Longqi Liu / Fengyu Hu / Dan Liang / Bixia Ke / Changwen Ke / Feng Li / Jun He / Meiniang Wang / Ling Chen / Xiaoli Xiong / Xiaoping Tang /
Abstract: SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading antibodies isolated earlier in the pandemic. Investigation of memory B cells from patients ...SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading antibodies isolated earlier in the pandemic. Investigation of memory B cells from patients primarily with breakthrough infections with the Delta variant enables isolation of a number of neutralizing antibodies cross-reactive to heterologous variants of concern (VOCs) including Omicron variants (BA.1-BA.4). Structural studies identify altered complementarity determining region (CDR) amino acids and highly unusual heavy chain CDR2 insertions respectively in two representative cross-neutralizing antibodies-YB9-258 and YB13-292. These features are putatively introduced by somatic hypermutation and they are heavily involved in epitope recognition to broaden neutralization breadth. Previously, insertions/deletions were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. These data provide molecular mechanisms for cross-neutralization of heterologous SARS-CoV-2 variants by antibodies isolated from Delta variant infected patients with implications for future vaccination strategy.
History
DepositionNov 1, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34655.png

Downloads & links

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Map

FileDownload / File: emd_34655.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused half map 2 of YB13-292 Fab complexed with Omicron S
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 256 pix.
= 422.4 Å		1.65 Å/pix.
x 256 pix.
= 422.4 Å		1.65 Å/pix.
x 256 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-6.4384313 - 8.551081999999999
Average (Standard dev.)0.0004225662 (±0.08550645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Focused map of YB13-292 Fab complexed with Omicron S

Fileemd_34655_half_map_1.map
AnnotationFocused map of YB13-292 Fab complexed with Omicron S
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused half map 1 of YB13-292 Fab complexed with Omicron S

Fileemd_34655_half_map_2.map
AnnotationFocused half map 1 of YB13-292 Fab complexed with Omicron S
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.1 spike trimer with in complex with YB13-29...

EntireName: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB13-292 Fab, focused refinement of Fab region
Components
  • Complex: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB13-292 Fab, focused refinement of Fab region
    • Complex: SARS-CoV-2 Omicron BA.1 spike protein
      • Protein or peptide: Spike protein S1
    • Complex: YB13-292 Fab
      • Protein or peptide: Heavy chain of YB13-292 Fab
      • Protein or peptide: Light chain of YB13-292 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB13-29...

SupramoleculeName: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB13-292 Fab, focused refinement of Fab region
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: SARS-CoV-2 Omicron BA.1 spike protein

SupramoleculeName: SARS-CoV-2 Omicron BA.1 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: YB13-292 Fab

SupramoleculeName: YB13-292 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.33207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ITNLCPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNL APFFTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKVSGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC NGVAGFNCYF P LRSYSFRP TYGVGHQPYR VVVLSFEL

UniProtKB: Spike glycoprotein

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Macromolecule #2: Heavy chain of YB13-292 Fab

MacromoleculeName: Heavy chain of YB13-292 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.283396 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCAASGFSFI TYNMNWVRQA PGKGLEWVSS ISSNILSSTS YIYYADSVKG RFTISRDDAA NSLFLQMNS LRVEDTAQYY CARTRSRSVR NCTSATCPVD AFDLWGQGTM VIVSSASTKG PSVFPLAPSS KSTSGGTAAL G CLVKDYFP ...String:
EVQLVESGGG LVKPGGSLRL SCAASGFSFI TYNMNWVRQA PGKGLEWVSS ISSNILSSTS YIYYADSVKG RFTISRDDAA NSLFLQMNS LRVEDTAQYY CARTRSRSVR NCTSATCPVD AFDLWGQGTM VIVSSASTKG PSVFPLAPSS KSTSGGTAAL G CLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD

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Macromolecule #3: Light chain of YB13-292 Fab

MacromoleculeName: Light chain of YB13-292 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.976648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVLTQSPLS LPVTPGEPAS ISCRSSQSLL RSNGYNYLDW YLQKPGQSPH LLIYLGSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PYTFGQGTNL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVLTQSPLS LPVTPGEPAS ISCRSSQSLL RSNGYNYLDW YLQKPGQSPH LLIYLGSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PYTFGQGTNL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

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

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Image processing

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

7t9k

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 210698
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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