+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28913 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 spike glycoprotein trimer bound with two nanobodies | |||||||||
Map data | Original, full map of SARS-CoV-2 spike glycoprotein trimer bound with two nanobodies. | |||||||||
Sample |
| |||||||||
Keywords | SARS-CoV-2 / spike / nanobody / antibody / 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: 3.58 Å | |||||||||
Authors | Laughlin ZT / Patel A / Ortlund EA | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: To Be Published Title: SARS-CoV-2 spike protein bound with nanobodies Authors: Laughlin ZT / Patel A / Ortlund EA | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28913.map.gz | 259.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28913-v30.xml emd-28913.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28913_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_28913.png | 119.2 KB | ||
Filedesc metadata | emd-28913.cif.gz | 6 KB | ||
Others | emd_28913_half_map_1.map.gz emd_28913_half_map_2.map.gz | 254.6 MB 254.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28913 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28913 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_28913.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Original, full map of SARS-CoV-2 spike glycoprotein trimer bound with two nanobodies. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0691 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half-map of original, full map of SARS-CoV-2 spike...
File | emd_28913_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map of original, full map of SARS-CoV-2 spike glycoprotein trimer bound with two nanobodies. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half-map of original, full map of SARS-CoV-2 spike...
File | emd_28913_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map of original, full map of SARS-CoV-2 spike glycoprotein trimer bound with two nanobodies. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike protein trimer with two spike protein-targeting ...
Entire | Name: SARS-CoV-2 spike protein trimer with two spike protein-targeting nanobodies attached on RBD domains. |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 spike protein trimer with two spike protein-targeting ...
Supramolecule | Name: SARS-CoV-2 spike protein trimer with two spike protein-targeting nanobodies attached on RBD domains. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|
-Supramolecule #2: Spike glycoprotein
Supramolecule | Name: Spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: Nanobody
Supramolecule | Name: Nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
---|---|
Source (natural) | Organism: Lama glama (llama) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
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: Anti-S1 Nanobody
Macromolecule | Name: Anti-S1 Nanobody / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Lama glama (llama) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGGTFS SIGMGWFRQA PGKEREFVAA ISWDGGATAY ADSVKGRFTI SADNSKNTAY LQMNSLKPE DTAVYYCAKE DVGKPFDWGQ GTLVTVSSG |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| |||||||||||||||
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 / Details: Wait time 20 seconds and blot time 3 seconds. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |
---|