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- EMDB-28930: SARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD i... -

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Basic information

Entry
Database: EMDB / ID: EMD-28930
TitleSARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD in "up" conformation
Map dataFull, original map SARS-CoV-2 spike glycoprotein trimer with a nanobody bound to an RBD in the up conformation
Sample
  • Complex: Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins
    • Complex: NanobodySingle-domain antibody
      • Protein or peptide: Anti-S1 Nanobody
    • Complex: Spike protein trimer
      • Protein or peptide: Spike glycoproteinSpike protein
KeywordsSARS-CoV-2 / spike / antibody / nanobody / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Biological speciesLama glama (llama) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsLaughlin ZT / Patel A / Ortlund EA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)3U54EB027690-04S United States
CitationJournal: To Be Published
Title: SARS-CoV-2 spike protein bound with nanobody
Authors: Laughlin ZL / Patel A / Ortlund EA
History
DepositionNov 22, 2022-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28930.png

Downloads & links

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Map

FileDownload / File: emd_28930.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull, original map SARS-CoV-2 spike glycoprotein trimer with a nanobody bound to an RBD in the up conformation
Voxel sizeX=Y=Z: 1.0691 Å
Density
Contour LevelBy AUTHOR: 0.0601
Minimum - Maximum-1.0123124 - 1.7334422
Average (Standard dev.)-0.0001807265 (±0.02482168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 444.7456 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of full, original map SARS-CoV-2 spike...

Fileemd_28930_half_map_1.map
AnnotationHalf map of full, original map SARS-CoV-2 spike glycoprotein trimer with a nanobody bound to an RBD in the up conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of full, original map SARS-CoV-2 spike...

Fileemd_28930_half_map_2.map
AnnotationHalf map of full, original map SARS-CoV-2 spike glycoprotein trimer with a nanobody bound to an RBD in the up conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins

EntireName: Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins
Components
  • Complex: Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins
    • Complex: NanobodySingle-domain antibody
      • Protein or peptide: Anti-S1 Nanobody
    • Complex: Spike protein trimer
      • Protein or peptide: Spike glycoproteinSpike protein

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Supramolecule #1: Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins

SupramoleculeName: Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Nanobody

SupramoleculeName: Nanobody / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

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Supramolecule #3: Spike protein trimer

SupramoleculeName: Spike protein trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
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 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVTKR FDNPVLPFND GVYFASTEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLGVYYHK NNKSWMESEF R VYSSANNC TFEYVSQPFL MDLEGKQGNF ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVTKR FDNPVLPFND GVYFASTEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLGVYYHK NNKSWMESEF R VYSSANNC TFEYVSQPFL MDLEGKQGNF KNLREFVFKN IDGYFKIYSK HTPINLVRDL PQGFSALEPL VD LPIGINI TRFQTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSE TKCTLK SFTVEKGIYQ TSNFRVQPTE SIVRFPNITN LCPFGEVFNA TRFASVYAWN RKRISNCVAD YSVL YNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYNY KLPDDFTGCV IAWNS NNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL QSYGFQPTNG VGYQPY RVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLTGTGV LTESNKKFLP FQQFGRDIAD TTDAVRD PQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCNVF QTRAGCLIGA EHVNNSYECD IPIGAGIC A SYQTSQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISVTT EILPVSMTKT SVDCTMYICG DSTECSNLL LQYGSFCTQL NRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKDFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTCAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQNV L YENQKLIA NQFNSAIGKI QDSLSSALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDILSRLDPP EA EVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PHG VVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVV IGIVN NTVYDPLQPE LD

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Macromolecule #2: Anti-S1 Nanobody

MacromoleculeName: Anti-S1 Nanobody / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCAASGGTFS SIGMGWFRQA PGKEREFVAA ISWDGGATAY ADSVKGRFTI SADNSKNTA YLQMNSLKPE DTAVYYCAKE DVGKPFDWGQ GTLVTVSSG

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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

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chlorideSodium chloride
2.7 mMKClPotassium chloride
8.0 mMNa2HPO4Sodium hydrogen Phosphate
2.0 mMKH2PO4Potassium Di-hydrogen Phosphate
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Slit width: 30 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4186 / Average electron dose: 63.81 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1725357
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 431339 / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 615492
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 102 / Target criteria: Correlation coefficient

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