+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28686 | |||||||||
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Title | SARS-CoV-2 spike protein complexed with two nanobodies | |||||||||
Map data | Composite map (made from other two submitted maps) of nanobodies bound to SARS-CoV-2 spike protein. | |||||||||
Sample |
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Keywords | SARS-CoV-2 / spike / nanobody / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information 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 ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.73 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 bound with nanobodies Authors: Laughlin ZT / Patel A / Ortlund EA | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28686.map.gz | 255.6 MB | EMDB map data format | |
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Header (meta data) | emd-28686-v30.xml emd-28686.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28686_fsc.xml emd_28686_fsc_2.xml | 13.8 KB 13.8 KB | Display Display | FSC data file |
Images | emd_28686.png | 143.5 KB | ||
Filedesc metadata | emd-28686.cif.gz | 7.2 KB | ||
Others | emd_28686_additional_1.map.gz emd_28686_additional_2.map.gz emd_28686_additional_3.map.gz emd_28686_additional_4.map.gz emd_28686_additional_5.map.gz emd_28686_additional_6.map.gz | 258.8 MB 259.4 MB 254.6 MB 254.6 MB 254.7 MB 254.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28686 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28686 | HTTPS FTP |
-Validation report
Summary document | emd_28686_validation.pdf.gz | 515 KB | Display | EMDB validaton report |
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Full document | emd_28686_full_validation.pdf.gz | 514.6 KB | Display | |
Data in XML | emd_28686_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | emd_28686_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28686 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28686 | HTTPS FTP |
-Related structure data
Related structure data | 8eygMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28686.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map (made from other two submitted maps) of nanobodies bound to SARS-CoV-2 spike protein. | ||||||||||||||||||||
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
-Additional map: Local-refined map of nanobodies bound to SARS-CoV-2 spike protein.
File | emd_28686_additional_1.map | ||||||||||||
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Annotation | Local-refined map of nanobodies bound to SARS-CoV-2 spike protein. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Original, overall map of nanobodies bound to SARS-CoV-2...
File | emd_28686_additional_2.map | ||||||||||||
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Annotation | Original, overall map of nanobodies bound to SARS-CoV-2 spike protein. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of original, overall map of nanobodies bound...
File | emd_28686_additional_3.map | ||||||||||||
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Annotation | Half-map of original, overall map of nanobodies bound to SARS-CoV-2 spike protein. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of original, overall map of nanobodies bound...
File | emd_28686_additional_4.map | ||||||||||||
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Annotation | Half-map of original, overall map of nanobodies bound to SARS-CoV-2 spike protein. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of original, overall map of nanobodies bound...
File | emd_28686_additional_5.map | ||||||||||||
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Annotation | Half-map of original, overall map of nanobodies bound to SARS-CoV-2 spike protein. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of original, overall map of nanobodies bound...
File | emd_28686_additional_6.map | ||||||||||||
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Annotation | Half-map of original, overall map of nanobodies bound to SARS-CoV-2 spike protein. | ||||||||||||
Projections & Slices |
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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. |
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Components |
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-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: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 125.882547 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 UniProtKB: Spike glycoprotein |
-Macromolecule #2: Nanobody
Macromolecule | Name: Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 12.360667 KDa |
Recombinant expression | Organism: Lama glama (llama) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGGTFS SIGMGWFRQA PGKEREFVAA ISWDGGATAY ADSVKGRFTI SADNSKNTAY LQMNSLKPE DTAVYYCAKE DVGKPFDWGQ GTLVTVSSG |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 25 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
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 |
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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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Output model | PDB-8eyg: |