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- EMDB-49461: GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein -

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Basic information

Entry
Database: EMDB / ID: EMD-49461
TitleGB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein
Map dataGB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein
Sample
  • Complex: GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein
    • Protein or peptide: SARS-CoV-2 BA.1 Spike protein
    • Protein or peptide: PRO-27522 light chain
    • Protein or peptide: PRO-27522 heavy chain
    • Protein or peptide: GB-0669 light chain
    • Protein or peptide: GB-0669 heavy chain
KeywordsSARS / Spike / Antibody / Inhibitor / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.19 Å
AuthorsZimmerman MI / Jecrois A
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein
Authors: Zimmerman MI / Jecrois A
History
DepositionFeb 26, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49461.png

Downloads & links

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Map

FileDownload / File: emd_49461.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 200 pix.
= 700. Å		3.5 Å/pix.
x 200 pix.
= 700. Å		3.5 Å/pix.
x 200 pix.
= 700. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-3.6269019 - 6.4904323
Average (Standard dev.)-0.0009153447 (±0.24304022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 700.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: GB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein (unsharpened)

Fileemd_49461_additional_1.map
AnnotationGB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein half map B

Fileemd_49461_half_map_1.map
AnnotationGB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein half map A

Fileemd_49461_half_map_2.map
AnnotationGB-0669 and PRO-37587 bound to SARS-CoV-2 spike protein half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein

EntireName: GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein
Components
  • Complex: GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein
    • Protein or peptide: SARS-CoV-2 BA.1 Spike protein
    • Protein or peptide: PRO-27522 light chain
    • Protein or peptide: PRO-27522 heavy chain
    • Protein or peptide: GB-0669 light chain
    • Protein or peptide: GB-0669 heavy chain

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Supramolecule #1: GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein

SupramoleculeName: GB-0669 and PRO-27522 bound to SARS-CoV-2 Spike protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SARS-CoV-2 BA.1 Spike protein

MacromoleculeName: SARS-CoV-2 BA.1 Spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLPPAYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHVISGTN GTKRFDNPVL PFNDGVYFAS IEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM DLEGKQGNFK NLREFVFKNI ...String:
QLPPAYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHVISGTN GTKRFDNPVL PFNDGVYFAS IEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM DLEGKQGNFK NLREFVFKNI DGYFKIYSKH TPIIVREPED LPQGFSALEP LVDLPIGINI TRFQTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPFDEVFNAT RFASVYAWNR KRISNCVADY SVLYNLAPFF TFKCYGVSPT KLNDLCFTNV YADSFVIRGD EVRQIAPGQT GNIADYNYKL PDDFTGCVIA WNSNKLDSKV SGNYNYLYRL FRKSNLKPFE RDISTEIYQA GNKPCNGVAG FNCYFPLRSY SFRPTYGVGH QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LKGTGVLTES NKKFLPFQQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHRAAA SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF KGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTPSAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS VLNDIFSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQPE

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Macromolecule #2: PRO-27522 light chain

MacromoleculeName: PRO-27522 light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TVLTQPPSVS GAPGQRVTIS CTGSSSNIGA GYRVHWYQQL PGTAPKLLIA GRSNRPSGVP DRFSGSKSGT SASLAITGLQ AEDEADYYCQ SYDSSLFDPH WVFGGGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP VKAGVETTTP ...String:
TVLTQPPSVS GAPGQRVTIS CTGSSSNIGA GYRVHWYQQL PGTAPKLLIA GRSNRPSGVP DRFSGSKSGT SASLAITGLQ AEDEADYYCQ SYDSSLFDPH WVFGGGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP VKAGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTE

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Macromolecule #3: PRO-27522 heavy chain

MacromoleculeName: PRO-27522 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVQSGAEV KKPGSSVKVS CKASGDTSDT YTISWVRQAP GQGLEWMGRI ILLSGYANYA QKIQGRVTIT ADKSTSTAYM ELTSLRSDDT AVYYCARGFN GDYYGWGDDD AFDFWGQGTL VTVYSASTKG PSVFPLAPSG TAALGCLVKD YFPEPVTVSW NSGALTSGVH ...String:
VQLVQSGAEV KKPGSSVKVS CKASGDTSDT YTISWVRQAP GQGLEWMGRI ILLSGYANYA QKIQGRVTIT ADKSTSTAYM ELTSLRSDDT AVYYCARGFN GDYYGWGDDD AFDFWGQGTL VTVYSASTKG PSVFPLAPSG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKRVEPK S

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Macromolecule #4: GB-0669 light chain

MacromoleculeName: GB-0669 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPSS VSASVGDRVT ITCRASQGIS SWLAWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQQ GHSFPYTFGQ GTNLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD ...String:
EIVLTQSPSS VSASVGDRVT ITCRASQGIS SWLAWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQQ GHSFPYTFGQ GTNLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGE

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Macromolecule #5: GB-0669 heavy chain

MacromoleculeName: GB-0669 heavy chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGAE VKKPGESLKI SCKGSGYTFT RYWIGWVRQM PGKGLEWMGI IYPGDSDVRY SPSFQGHVTI SADKSISTAY LQWNSLKASD TAMYYCARLP QYCSKGVCYR WFDPWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA ...String:
EVQLVESGAE VKKPGESLKI SCKGSGYTFT RYWIGWVRQM PGKGLEWMGI IYPGDSDVRY SPSFQGHVTI SADKSISTAY LQWNSLKASD TAMYYCARLP QYCSKGVCYR WFDPWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPK

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationName
50.0 mMtris(hydroxymethyl)aminomethane hydrochloride
300.0 mMsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5157
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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