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- EMDB-49799: SARS-CoV-2 BA.1 S6P (HexaPro) + COV2-3835 Fab Global Map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49799
TitleSARS-CoV-2 BA.1 S6P (HexaPro) + COV2-3835 Fab Global Map
Map dataGlobal map sharpened
Sample
  • Complex: SARS-CoV-2 BA.1 S6P (HexaPro) + COV2-3835 Fab
    • Complex: SARS-CoV-2 BA.1 S6P (HexaPro)
      • Protein or peptide: SARS-CoV-2 BA.1 Spike (HexaPro)
    • Complex: COV2-3835 Fab
      • Protein or peptide: COV2-3835 Fab Heavy Chain
      • Protein or peptide: COV2-3835 Fab Light Chain
KeywordsSARS-CoV-2 / Omicron / RBD / Fab / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRamamohan AR / Johnson NV / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants
Authors: Ramamohan AR / Johnson NV / McLellan JS
History
DepositionMar 19, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49799.png

Downloads & links

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Map

FileDownload / File: emd_49799.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal map sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 430.08 Å		0.84 Å/pix.
x 512 pix.
= 430.08 Å		0.84 Å/pix.
x 512 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-1.0728357 - 1.8949202
Average (Standard dev.)-0.00026863604 (±0.028907066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_49799_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_49799_half_map_2.map
AnnotationHalf map B
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 BA.1 S6P (HexaPro) + COV2-3835 Fab

EntireName: SARS-CoV-2 BA.1 S6P (HexaPro) + COV2-3835 Fab
Components
  • Complex: SARS-CoV-2 BA.1 S6P (HexaPro) + COV2-3835 Fab
    • Complex: SARS-CoV-2 BA.1 S6P (HexaPro)
      • Protein or peptide: SARS-CoV-2 BA.1 Spike (HexaPro)
    • Complex: COV2-3835 Fab
      • Protein or peptide: COV2-3835 Fab Heavy Chain
      • Protein or peptide: COV2-3835 Fab Light Chain

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Supramolecule #1: SARS-CoV-2 BA.1 S6P (HexaPro) + COV2-3835 Fab

SupramoleculeName: SARS-CoV-2 BA.1 S6P (HexaPro) + COV2-3835 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SARS-CoV-2 BA.1 S6P (HexaPro)

SupramoleculeName: SARS-CoV-2 BA.1 S6P (HexaPro) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: COV2-3835 Fab

SupramoleculeName: COV2-3835 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SARS-CoV-2 BA.1 Spike (HexaPro)

MacromoleculeName: SARS-CoV-2 BA.1 Spike (HexaPro) / type: protein_or_peptide / ID: 1 / Details: Trimeric viral fusion protein ectodomain / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVYF ASIEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD HKNNKSWMES EFRVYSSANN CTFEYVSQPF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVYF ASIEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD HKNNKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLREFVFK NIDGYFKIYS KHTPIIVREP EDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SSSGWTAGAA AYYVGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNLAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYNY KLPDDFTGCV IAWNSNKLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGFNCYFPLR SYSFRPTYGV GHQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLKGTGVLT ESNKKFLPFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ GVNCTEVPVA IHADQLTPTW RVYSTGSNVF QTRAGCLIGA EYVNNSYECD IPIGAGICAS YQTQTKSHGS ASSVASQSII AYTMSLGAEN SVAYSNNSIA IPTNFTISVT TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFKGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGPA LQIPFPMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLSSTPS ALGKLQDVVN HNAQALNTLV KQLSSKFGAI SSVLNDIFSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNCDVVIGIV NNTVYDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQGSGYI PEAPRDGQAY VRKDGEWVLL STFLGRSLEV LFQGPGHHHH HHHHSAWSHP QFEKGGGSGG GGSGGSAWSH PQFEK

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Macromolecule #2: COV2-3835 Fab Heavy Chain

MacromoleculeName: COV2-3835 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Details: Human IgG Antibody / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QITLKESGPT LVKPTQTLTL TCTFSGFSLS TSGVGVGWIR QPPGQALECL SLIYWNDDKR YSPSLKTRLT VTKDTSKNQV VLRMTNMDPV DTATYYCAHI GTDLLTGFWT DAFEIWGQGT MVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG ...String:
QITLKESGPT LVKPTQTLTL TCTFSGFSLS TSGVGVGWIR QPPGQALECL SLIYWNDDKR YSPSLKTRLT VTKDTSKNQV VLRMTNMDPV DTATYYCAHI GTDLLTGFWT DAFEIWGQGT MVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSC

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Macromolecule #3: COV2-3835 Fab Light Chain

MacromoleculeName: COV2-3835 Fab Light Chain / type: protein_or_peptide / ID: 3 / Details: Human IgG Antibody / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKVPKLLIYA ASSLQSGVPP RFSGSGSGTD FTLTISTLQP EDFATYYCQQ SYGMLWTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKVPKLLIYA ASSLQSGVPP RFSGSGSGTD FTLTISTLQP EDFATYYCQQ SYGMLWTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LRSPVTKSFN RGEC

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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

Concentration0.65 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was monodisperse. Mixed occupancy of Fabs bound to SARS-CoV-2 spike.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction in CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152740
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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