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- EMDB-24729: CryoEM structure of RBD domain of COVID-19 in complex with Legobody -

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Basic information

Entry
Database: EMDB / ID: EMD-24729
TitleCryoEM structure of RBD domain of COVID-19 in complex with Legobody
Map datasharpened map for the complex
Sample
  • Complex: The complex of RBD domain of COVID-19 with Legobody
    • Protein or peptide: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
    • Protein or peptide: Fab_8D3_2 heavy chain
    • Protein or peptide: Fab_8D3_2 light chain
    • Protein or peptide: Nb_RBD
    • Protein or peptide: Spike protein S1
KeywordsRBD / maltose-binding protein / Fab / nanobody / STRUCTURAL PROTEIN
Function / homology
Function and homology information


IgG binding / carbohydrate transmembrane transporter activity / 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 ...IgG binding / carbohydrate transmembrane transporter activity / 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 / periplasmic space / 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 / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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
Maltodextrin-binding protein / Immunoglobulin G-binding protein G / Spike glycoprotein / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria) / Mus musculus (house mouse) / Vicugna pacos (alpaca) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWu XD / Rapoport TA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM052586 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies).
Authors: Xudong Wu / Tom A Rapoport /
Abstract: We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding ...We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody-target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.
History
DepositionAug 22, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rxd
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24729.png

Downloads & links

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Map

FileDownload / File: emd_24729.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map for the complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 230 pix.
= 243.8 Å		1.06 Å/pix.
x 230 pix.
= 243.8 Å		1.06 Å/pix.
x 230 pix.
= 243.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.16285487 - 0.23269646
Average (Standard dev.)0.0001092493 (±0.004385743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 243.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z243.800243.800243.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.1630.2330.000

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Supplemental data

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Additional map: unsharpened map

Fileemd_24729_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of RBD domain of COVID-19 with Legobody

EntireName: The complex of RBD domain of COVID-19 with Legobody
Components
  • Complex: The complex of RBD domain of COVID-19 with Legobody
    • Protein or peptide: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
    • Protein or peptide: Fab_8D3_2 heavy chain
    • Protein or peptide: Fab_8D3_2 light chain
    • Protein or peptide: Nb_RBD
    • Protein or peptide: Spike protein S1

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Supramolecule #1: The complex of RBD domain of COVID-19 with Legobody

SupramoleculeName: The complex of RBD domain of COVID-19 with Legobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,I...

MacromoleculeName: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sp. (bacteria)
Molecular weightTheoretical: 59.233246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDQALAFAQ ILIMPNLTEE QRNGFIQSLK DDPSVSKEIL AEAK KLNEH QAPKGGSGGA GSGDQQSAFY EILNMPNLNE AQRNGFIQSL KDDPSQSTNV LGEAKKLNES QAGGGSGGGS GGSAV TTYK LVINGKTLKG ETTTKAVDAE TAEKAFKQYA NDNGVDGVWT YDDATKTFTV TEGSGHHHHH H

UniProtKB: Maltodextrin-binding protein, Immunoglobulin G-binding protein A, Immunoglobulin G-binding protein G

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Macromolecule #2: Fab_8D3_2 heavy chain

MacromoleculeName: Fab_8D3_2 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.252217 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLVESGGG LVQPGKSLRL SCAASGFTFS NFGMHWVRQA PEMGLEWVAY ISSGSTTKYY GDTVKGRFTI SRDNPKNTLY LQMNSLRSE DTAMYYCARR PLYDGDYGYP MDYWGQGTSV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
DVQLVESGGG LVQPGKSLRL SCAASGFTFS NFGMHWVRQA PEMGLEWVAY ISSGSTTKYY GDTVKGRFTI SRDNPKNTLY LQMNSLRSE DTAMYYCARR PLYDGDYGYP MDYWGQGTSV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCGS HHHHHH

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Macromolecule #3: Fab_8D3_2 light chain

MacromoleculeName: Fab_8D3_2 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.095852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NIMLTQSPSS LAVSAGERVT MSCKSTQSIL YNSNQKTYLA WYQQKPGQSP KLLIYWASTR ASGVPDRFTG SGSGTDFTLT INSVQPEDL AVYYCHQYLS AWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
NIMLTQSPSS LAVSAGERVT MSCKSTQSIL YNSNQKTYLA WYQQKPGQSP KLLIYWASTR ASGVPDRFTG SGSGTDFTLT INSVQPEDL AVYYCHQYLS AWTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #4: Nb_RBD

MacromoleculeName: Nb_RBD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.661201 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGFPVY RDRMAWYRQA PGKEREWVAA IYSAGQQTRY ADSVKGRFTI SRDNAKNTVY LQMNSLKPE DTAVYYCNVK DVGHHYEYYD YWGQGTQVTV SSLEHHHHHH

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Macromolecule #5: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.995555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDYKDDDDKG GENLYFQGGS GDSTGSSNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNV YADSFVIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE R DISTEIYQ ...String:
GDYKDDDDKG GENLYFQGGS GDSTGSSNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNV YADSFVIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE R DISTEIYQ AGSTPCNGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGGGGSGSGH HHHHHHH

UniProtKB: Spike glycoprotein

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.42 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282995
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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