+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33550 | |||||||||
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Title | SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / spike / bispecific antibody / SYZJ001 / R15-F7 / P14-F8-35 / STRUCTURAL PROTEIN / 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 / 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 / Vicugna pacos (alpaca) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Wang L / Zhu L | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody Authors: Wang L | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33550.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-33550-v30.xml emd-33550.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_33550.png | 23.3 KB | ||
Others | emd_33550_half_map_1.map.gz emd_33550_half_map_2.map.gz | 165.3 MB 165.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33550 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33550 | HTTPS FTP |
-Validation report
Summary document | emd_33550_validation.pdf.gz | 808.6 KB | Display | EMDB validaton report |
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Full document | emd_33550_full_validation.pdf.gz | 808.2 KB | Display | |
Data in XML | emd_33550_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_33550_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33550 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33550 | HTTPS FTP |
-Related structure data
Related structure data | 7y0nMC 7y0oC 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_33550.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33550_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33550_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35
Entire | Name: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35 |
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Components |
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-Supramolecule #1: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35
Supramolecule | Name: Complex of SARS-CoV-2 Spike in complex with R15-F7 and P14-F18-35 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #4 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: SARS-CoV-2 Spike
Supramolecule | Name: SARS-CoV-2 Spike / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Supramolecule #3: P14
Supramolecule | Name: P14 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #4: R15-F7
Supramolecule | Name: R15-F7 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2, #4 |
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-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: 127.076031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNEVAVLYQ DVNCTEVFVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPR RARSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STASALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD S UniProtKB: Spike glycoprotein |
-Macromolecule #2: Heavy chain of R15-F7
Macromolecule | Name: Heavy chain of R15-F7 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.638069 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QMQLVQSGAE VKKPGASVKV SCKASGYTFT SYAISWVRQA PGQGLEWMGR IIPILGIANY AQKFQGRVTI TADESTSTAY MELSSRSED TAVYYCASGA FYYGSGSYPF DYWGQGT |
-Macromolecule #3: P14 Nanobody
Macromolecule | Name: P14 Nanobody / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 13.461807 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EEQLVESGGG LVQPGGSLRL SCAASGFRFG SYYMSWVRQA PGKAPEWVSD INTRGETTRY SDSVKGRFTI ARDNANNTVF LFMNRLKPE DTAVYYCAVA ASGDTFEGRS DPDYWGQGTL VTVS |
-Macromolecule #4: Light chain of R15-F7
Macromolecule | Name: Light chain of R15-F7 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.675858 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GDIQLTQSPS SLSASVGDRV TITCRASQDI SDYLNWYQQK PGKAPKLLIY AASSLQSGVP SRFSGSGSGT DFTLTISNLQ PEDFATYYC QQSYSAPRTF GQGTKVEIK |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 33 / 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
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 372940 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |