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Yorodumi- EMDB-31390: CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31390 | |||||||||
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Title | CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 Fab and BD-836 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 | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Liu PL | |||||||||
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_31390.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-31390-v30.xml emd-31390.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_31390.png | 89.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31390 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31390 | HTTPS FTP |
-Validation report
Summary document | emd_31390_validation.pdf.gz | 349.9 KB | Display | EMDB validaton report |
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Full document | emd_31390_full_validation.pdf.gz | 349.5 KB | Display | |
Data in XML | emd_31390_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_31390_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31390 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31390 | HTTPS FTP |
-Related 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_31390.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: 1.08 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 : CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 F...
Entire | Name: CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 Fab and BD-836 Fab |
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Components |
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-Supramolecule #1: CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 F...
Supramolecule | Name: CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 Fab and BD-836 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Phaseolus vulgaris (French bean) |
-Macromolecule #1: spike
Macromolecule | Name: spike / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
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-812L
Macromolecule | Name: BD-812L / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MGWSCIILFL VATATGVHSD IEITQSPSSL SASVGDRVTI SCRASQDIRT YVAWYQQRPG KVPRLLIYAA STLQSGVPSR FSGRGSGTDF TLTISSLQPE DVATYYCQQY NSAPLTFGGG AKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD ...String: MGWSCIILFL VATATGVHSD IEITQSPSSL SASVGDRVTI SCRASQDIRT YVAWYQQRPG KVPRLLIYAA STLQSGVPSR FSGRGSGTDF TLTISSLQPE DVATYYCQQY NSAPLTFGGG AKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE SVTEQDSKDS TYSLSSTLTL SKADYEKHKV YACEVTHQGL SSPVTKSFNR GEC |
-Macromolecule #3: BD-812H
Macromolecule | Name: BD-812H / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MGWSLILLFL VAVATRVLSE VQLVQSGAEV KKPGESLKIS CQFSEYKLIS FWIAWVRQRP GKGLEWMGII YPDDSDTKYS PSSQGQVTIS ADKSIRTAYL QWSSLMASDT AMYYCTSGSY YGTLDFWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF ...String: MGWSLILLFL VAVATRVLSE VQLVQSGAEV KKPGESLKIS CQFSEYKLIS FWIAWVRQRP GKGLEWMGII YPDDSDTKYS PSSQGQVTIS ADKSIRTAYL QWSSLMASDT AMYYCTSGSY YGTLDFWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC DKHHHHHH |
-Macromolecule #4: BD-836L
Macromolecule | Name: BD-836L / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MGWSCIILFL VATATGVHSE IVLTQSPGTL SLSPGERATL SCRASQSVRS GYFAWYQQRP GRAPRLLIYG ASSRATAIPD RFSGSGSGTD FTLTINRLEP EDFAVYYCQQ YGTSPWTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV ...String: MGWSCIILFL VATATGVHSE IVLTQSPGTL SLSPGERATL SCRASQSVRS GYFAWYQQRP GRAPRLLIYG ASSRATAIPD RFSGSGSGTD FTLTINRLEP EDFAVYYCQQ YGTSPWTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC |
-Macromolecule #5: BD-836H
Macromolecule | Name: BD-836H / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MGWSLILLFL VAVATRVLSQ VQLVQSGPEV KKPGTSVRVS CKASGFTFST SAVQWVRQAR GQRLEWIGWI AVGSGKTDYL QKFQERVTMT RDESTNTAYM QLSSLRSEDT AVYYCAAPHC SGGTCYDGFD IWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL ...String: MGWSLILLFL VAVATRVLSQ VQLVQSGPEV KKPGTSVRVS CKASGFTFST SAVQWVRQAR GQRLEWIGWI AVGSGKTDYL QKFQERVTMT RDESTNTAYM QLSSLRSEDT AVYYCAAPHC SGGTCYDGFD IWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKHHH HHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.2 |
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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: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 257589 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |