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Yorodumi- EMDB-31378: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31378 | |||||||||
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Title | Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab | |||||||||
Map data | ||||||||||
Sample |
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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 / symbiont-mediated suppression of host innate immune response / 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 | Human coronavirus 229E / Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / Resolution: 3.4 Å | |||||||||
Authors | Zhang ZY | |||||||||
Citation | Journal: Cell Res / Year: 2021 Title: Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants. Authors: Shuo Du / Pulan Liu / Zhiying Zhang / Tianhe Xiao / Ayijiang Yasimayi / Weijin Huang / Youchun Wang / Yunlong Cao / Xiaoliang Sunney Xie / Junyu Xiao / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31378.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-31378-v30.xml emd-31378.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
Images | emd_31378.png | 30.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31378 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31378 | HTTPS FTP |
-Validation report
Summary document | emd_31378_validation.pdf.gz | 399.7 KB | Display | EMDB validaton report |
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Full document | emd_31378_full_validation.pdf.gz | 399.3 KB | Display | |
Data in XML | emd_31378_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_31378_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31378 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31378 | HTTPS FTP |
-Related structure data
Related structure data | 7ey5MC 7ey0C 7ey4C 7eyaC 7ezvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_31378.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD...
Entire | Name: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab |
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Components |
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-Supramolecule #1: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD...
Supramolecule | Name: Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human coronavirus 229E |
Recombinant expression | Organism: Phaseolus vulgaris (French bean) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 142.066094 KDa |
Recombinant expression | Organism: Phaseolus vulgaris (French bean) |
Sequence | String: MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRGLPQ GFSALEPLVD LPIGINITRF QT LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGV KGFN CYFPLQSYGF QPTYGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEH VNNSYECDIP IGAGICASYQ TQTNSPGSAS SVASQSIIAY TMSLGVENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NQNAQALNTL V KQLSSNFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSH PQFE K |
-Macromolecule #2: BD-821H
Macromolecule | Name: BD-821H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.878969 KDa |
Recombinant expression | Organism: Phaseolus vulgaris (French bean) |
Sequence | String: ELQLVQSGAE VKKPGESLKI SCKYSGNISP NFWIGWVRQM AGKGLEWMGI IYPDDSDSRY SPSFQGQVII SADKSITTAL LHWSSLKVS DTAKYYCVYG SGSPSNWFHP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String: ELQLVQSGAE VKKPGESLKI SCKYSGNISP NFWIGWVRQM AGKGLEWMGI IYPDDSDSRY SPSFQGQVII SADKSITTAL LHWSSLKVS DTAKYYCVYG SGSPSNWFHP WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKHHH HHH |
-Macromolecule #3: BD-821L
Macromolecule | Name: BD-821L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.689248 KDa |
Recombinant expression | Organism: Phaseolus vulgaris (French bean) |
Sequence | String: EVVMTQSPAT LSVSPGERAT LSCRASQSVR YNLAWYQQKP GQAPRLLIYD ASTRATGIPG RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYDNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: EVVMTQSPAT LSVSPGERAT LSCRASQSVR YNLAWYQQKP GQAPRLLIYD ASTRATGIPG RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYDNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: BD-771H
Macromolecule | Name: BD-771H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.0751 KDa |
Recombinant expression | Organism: Phaseolus vulgaris (French bean) |
Sequence | String: EVQLVESGGG FVKPGGSLRL SCAASGFKFS DAWMNWVRQA PGKGLEWVGR IKSKADGQTT DYAAPVKGRF SISRDDSKNT LFLQIHNLE SDDTAVYYCT TGALVESRYF DWFTGYYFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String: EVQLVESGGG FVKPGGSLRL SCAASGFKFS DAWMNWVRQA PGKGLEWVGR IKSKADGQTT DYAAPVKGRF SISRDDSKNT LFLQIHNLE SDDTAVYYCT TGALVESRYF DWFTGYYFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKHHH HH H |
-Macromolecule #5: BD-771L
Macromolecule | Name: BD-771L / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.281967 KDa |
Recombinant expression | Organism: Phaseolus vulgaris (French bean) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRTSQGIY NYLAWYQQKP GKVPKLLIYG ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYKSAPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASVGDRVT ITCRTSQGIY NYLAWYQQKP GKVPKLLIYG ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYKSAPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 425986 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |