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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: Nanobody
      • Protein or peptide: Anti-S1 Nanobody
    • Complex: Spike protein trimer
      • Protein or peptide: Spike glycoprotein
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: Biorxiv / Year: 2024
Title: Structural basis of SARS-Cov-2 spike recognition by engineered synthetic multivalent VHH antibodies
Authors: Lujan Hernandez AG / Laughlin ZT / Patel A / Yuan TZ / Nugent RL / Axelrod F / Ortlund EA / Sato AK
History
DepositionNov 22, 2022-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing 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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 416 pix.
= 444.746 Å		1.07 Å/pix.
x 416 pix.
= 444.746 Å		1.07 Å/pix.
x 416 pix.
= 444.746 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0691 Å
Density

Histogram

Histogram (log scale)
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: Nanobody
      • Protein or peptide: Anti-S1 Nanobody
    • Complex: Spike protein trimer
      • Protein or peptide: Spike glycoprotein

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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 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
Specialist opticsEnergy filter - Slit width: 30 eV
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1725357
Startup modelType of model: OTHER
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 431339 / Software - Name: cryoSPARC (ver. 3.3.1)
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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