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- EMDB-28931: SARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD i... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | SARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD in the "up" conformation (locally-refined) | |||||||||
![]() | Locally-refined map of SARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD in the "up" conformation | |||||||||
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![]() | SARS-CoV-2 / spike / antibody / nanobody / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.53 Å | |||||||||
![]() | Laughlin ZT / Patel A / Ortlund EA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: SARS-CoV-2 spike protein bound with nanobody Authors: Laughlin ZL / Patel A / Ortlund EA | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 258.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.4 KB 18.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.8 KB | Display | ![]() |
Images | ![]() | 97 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 254.9 MB 254.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 798.4 KB | Display | ![]() |
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Full document | ![]() | 798 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Locally-refined map of SARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD in the "up" conformation | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0691 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map of locally-refined map of SARS-CoV-2 spike glycoprotein...
File | emd_28931_half_map_1.map | ||||||||||||
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Annotation | Half-map of locally-refined map of SARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD in the "up" conformation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map of locally-refined map of SARS-CoV-2 spike glycoprotein...
File | emd_28931_half_map_2.map | ||||||||||||
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Annotation | Half-map of locally-refined map of SARS-CoV-2 spike glycoprotein trimer with nanobody bound to RBD in the "up" conformation | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins
Entire | Name: Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins |
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Components |
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-Supramolecule #1: Complex of a nanobody bound to a trimer of SARS-CoV-2 spike proteins
Supramolecule | Name: 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
Supramolecule | Name: Nanobody / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Spike protein trimer
Supramolecule | Name: Spike protein trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: 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 |
-Macromolecule #2: Anti-S1 Nanobody
Macromolecule | Name: Anti-S1 Nanobody / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGGTFS SIGMGWFRQA PGKEREFVAA ISWDGGATAY ADSVKGRFTI SADNSKNTA YLQMNSLKPE DTAVYYCAKE DVGKPFDWGQ GTLVTVSSG |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.7 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4186 / Average electron dose: 63.81 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 102 / Target criteria: Correlation coefficient |
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