[English] 日本語
Yorodumi- EMDB-24729: CryoEM structure of RBD domain of COVID-19 in complex with Legobody -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24729 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of RBD domain of COVID-19 in complex with Legobody | |||||||||
Map data | sharpened map for the complex | |||||||||
Sample |
| |||||||||
Keywords | RBD / maltose-binding protein / Fab / nanobody / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information IgG binding / carbohydrate transmembrane transporter activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion ...IgG binding / carbohydrate transmembrane transporter activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / periplasmic space / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / 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 | |||||||||
Biological species | Streptococcus sp. (bacteria) / Mus musculus (house mouse) / Vicugna pacos (alpaca) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wu XD / Rapoport TA | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24729.map.gz | 43.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-24729-v30.xml emd-24729.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_24729.png | 45.9 KB | ||
Filedesc metadata | emd-24729.cif.gz | 6.2 KB | ||
Others | emd_24729_additional_1.map.gz | 35.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24729 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24729 | HTTPS FTP |
-Validation report
Summary document | emd_24729_validation.pdf.gz | 520.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_24729_full_validation.pdf.gz | 519.8 KB | Display | |
Data in XML | emd_24729_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_24729_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24729 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24729 | HTTPS FTP |
-Related structure data
Related structure data | 7rxdMC 7r9dC 7rxcC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_24729.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened map for the complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: unsharpened map
File | emd_24729_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : The complex of RBD domain of COVID-19 with Legobody
Entire | Name: The complex of RBD domain of COVID-19 with Legobody |
---|---|
Components |
|
-Supramolecule #1: The complex of RBD domain of COVID-19 with Legobody
Supramolecule | Name: The complex of RBD domain of COVID-19 with Legobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Maltodextrin-binding protein,Immunoglobulin G-binding protein A,I...
Macromolecule | Name: 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 weight | Theoretical: 59.233246 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Fab_8D3_2 heavy chain
Macromolecule | Name: 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 weight | Theoretical: 25.252217 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: Fab_8D3_2 light chain
Macromolecule | Name: 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 weight | Theoretical: 24.095852 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: Nb_RBD
Macromolecule | Name: Nb_RBD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 14.661201 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLVESGGG LVQAGGSLRL SCAASGFPVY RDRMAWYRQA PGKEREWVAA IYSAGQQTRY ADSVKGRFTI SRDNAKNTVY LQMNSLKPE DTAVYYCNVK DVGHHYEYYD YWGQGTQVTV SSLEHHHHHH |
-Macromolecule #5: Spike protein S1
Macromolecule | Name: 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 weight | Theoretical: 25.995555 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.42 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282995 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |