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Yorodumi- EMDB-28880: Locally refined map of SARS-CoV-2 spike glycoprotein trimer with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28880 | |||||||||
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Title | Locally refined map of SARS-CoV-2 spike glycoprotein trimer with nanobody bound to two RBDs | |||||||||
Map data | Locally-refined map of SARS-CoV-2 spike glycoprotein trimer (with RBDs in the down position) with a nanobody bound to two RBDs. | |||||||||
Sample |
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Keywords | SARS-CoV-2 / spike / antibody / nanobody / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.92 Å | |||||||||
Authors | Laughlin ZT / Patel A / Ortlund EA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: SARS-CoV-2 spike protein (down conformation) bound with a 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 | emd_28880.map.gz | 259 MB | EMDB map data format | |
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Header (meta data) | emd-28880-v30.xml emd-28880.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28880_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_28880.png | 85.3 KB | ||
Filedesc metadata | emd-28880.cif.gz | 6 KB | ||
Others | emd_28880_half_map_1.map.gz emd_28880_half_map_2.map.gz | 254.6 MB 254.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28880 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28880 | HTTPS FTP |
-Validation report
Summary document | emd_28880_validation.pdf.gz | 754.2 KB | Display | EMDB validaton report |
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Full document | emd_28880_full_validation.pdf.gz | 753.7 KB | Display | |
Data in XML | emd_28880_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | emd_28880_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28880 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28880 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28880.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Locally-refined map of SARS-CoV-2 spike glycoprotein trimer (with RBDs in the down position) with a nanobody bound to two RBDs. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_28880_half_map_1.map | ||||||||||||
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Annotation | Half-map of locally-refined map of SARS-CoV-2 spike glycoprotein trimer (with RBDs in the down position) with a nanobody bound to two RBDs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map of locally-refined map of SARS-CoV-2 spike glycoprotein...
File | emd_28880_half_map_2.map | ||||||||||||
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Annotation | Half-map of locally-refined map of SARS-CoV-2 spike glycoprotein trimer (with RBDs in the down position) with a nanobody bound to two RBDs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: Spike glycoprotein trimer
Supramolecule | Name: Spike glycoprotein trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: Nanobody
Supramolecule | Name: Nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Lama glama (llama) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Sequence | String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG ...String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GD SSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NIT NLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPG QTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQ SYGF QPTNGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQQFGR DIADTT DAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQDVN CTEVPVAIHA DQLTPTWRVY STGSNVFQTR AGCLIGA EH VNNSYECDIP IGAGICASYQ TQTNSPRRAR SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTK T SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFSQ ILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGPA LQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NQNAQALNTL VKQLSSNFGA I SSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FP QSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIV NNTVYD PLQPELDSFK |
-Macromolecule #2: Nanobody
Macromolecule | Name: Nanobody / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: FIELD EMISSION GUN |
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 |
+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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