+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28688 | |||||||||
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Title | SARS-CoV-2 spike protein bound with a nanobody | |||||||||
Map data | Composite map (made from other two uploaded maps) of SARS-CoV-2 spike protein trimer with nanobody bound. | |||||||||
Sample |
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Keywords | SARS-CoV-2 / spike / antibody / nanobody / 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 / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Vicugna pacos (alpaca) / Severe acute respiratory syndrome coronavirus 2 / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 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 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_28688.map.gz | 255.8 MB | EMDB map data format | |
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Header (meta data) | emd-28688-v30.xml emd-28688.xml | 28.9 KB 28.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28688_fsc.xml emd_28688_fsc_2.xml | 13.8 KB 13.8 KB | Display Display | FSC data file |
Images | emd_28688.png | 91.2 KB | ||
Filedesc metadata | emd-28688.cif.gz | 7.2 KB | ||
Others | emd_28688_additional_1.map.gz emd_28688_additional_2.map.gz emd_28688_additional_3.map.gz emd_28688_additional_4.map.gz emd_28688_additional_5.map.gz emd_28688_additional_6.map.gz | 258.9 MB 259.5 MB 254.6 MB 254.6 MB 254.9 MB 254.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28688 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28688 | HTTPS FTP |
-Related structure data
Related structure data | 8eyhMC 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_28688.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 uploaded maps) of SARS-CoV-2 spike protein trimer with nanobody bound. | ||||||||||||||||||||
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 SARS-CoV-2 spike protein trimer with...
File | emd_28688_additional_1.map | ||||||||||||
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Annotation | Local-refined map of SARS-CoV-2 spike protein trimer with nanobody bound. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Original map of SARS-CoV-2 spike protein trimer with nanobody bound.
File | emd_28688_additional_2.map | ||||||||||||
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Annotation | Original map of SARS-CoV-2 spike protein trimer with nanobody bound. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of original map of SARS-CoV-2 spike protein...
File | emd_28688_additional_3.map | ||||||||||||
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Annotation | Half-map of original map of SARS-CoV-2 spike protein trimer with nanobody bound. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of original map of SARS-CoV-2 spike protein...
File | emd_28688_additional_4.map | ||||||||||||
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Annotation | Half-map of original map of SARS-CoV-2 spike protein trimer with nanobody bound. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of local-refined map of SARS-CoV-2 spike protein...
File | emd_28688_additional_5.map | ||||||||||||
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Annotation | Half-map of local-refined map of SARS-CoV-2 spike protein trimer with nanobody bound. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half-map of local-refined map of SARS-CoV-2 spike protein...
File | emd_28688_additional_6.map | ||||||||||||
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Annotation | Half-map of local-refined map of SARS-CoV-2 spike protein trimer with nanobody bound. | ||||||||||||
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: #1-#2 |
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-Supramolecule #2: Nanobody
Supramolecule | Name: Nanobody / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Supramolecule #3: Spike protein trimer
Supramolecule | Name: Spike protein trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Nanobody
Macromolecule | Name: Nanobody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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 #2: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 2 / 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 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 24 / 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Slit width: 30 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
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 |
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-8eyh: |