+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33725 | |||||||||
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Title | SARS-CoV-2 B.1.620 variant spike (close state) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / Lambda / spike / VIRAL PROTEIN | |||||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / 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 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang X / Fu W | |||||||||
Funding support | 1 items
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Citation | Journal: Virol Sin / Year: 2022 Title: Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants. Authors: Xiaorui Xing / Lei Wang / Zhen Cui / Wangjun Fu / Tao Zheng / Lili Qin / Pingju Ge / Aidong Qian / Nan Wang / Shuai Yuan / Abstract: • Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift. • T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more ...• Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift. • T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more difficult. • The overall structures of the closed state S complex from different variants resemble each other. • Mutations in FPPR may affect the overall structure of the trimeric spike protein. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33725.map.gz | 117.2 MB | EMDB map data format | |
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Header (meta data) | emd-33725-v30.xml emd-33725.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_33725.png | 57.2 KB | ||
Filedesc metadata | emd-33725.cif.gz | 6.1 KB | ||
Others | emd_33725_half_map_1.map.gz emd_33725_half_map_2.map.gz | 98 MB 98 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33725 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33725 | HTTPS FTP |
-Validation report
Summary document | emd_33725_validation.pdf.gz | 751.1 KB | Display | EMDB validaton report |
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Full document | emd_33725_full_validation.pdf.gz | 750.7 KB | Display | |
Data in XML | emd_33725_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_33725_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33725 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33725 | HTTPS FTP |
-Related structure data
Related structure data | 7yblMC 7ybhC 7ybiC 7ybjC 7ybkC 7ybmC 7ybnC 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_33725.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_33725_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33725_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 B.1.620 variant spike (close state)
Entire | Name: SARS-CoV-2 B.1.620 variant spike (close state) |
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Components |
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-Supramolecule #1: SARS-CoV-2 B.1.620 variant spike (close state)
Supramolecule | Name: SARS-CoV-2 B.1.620 variant spike (close state) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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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: 140.983031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPSAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNAVIKVC EFQFCNDPFL GVDELYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNLTT RTQLPSAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNAVIKVC EFQFCNDPFL GVDELYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LYRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGNT PCNGV KGFN CYFPLQSYGF QPTNGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEH VNNSYECDIP IGAGICASYQ TQTNSHRRAR SVASQSIIAY TMSLGAENSV 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 ANLAAIKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTHNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ YIKWPWYIWL GFIAGLIAIV MVTIMLCCMT SCCSCLKGCC SCGSCCKFDE DDSEPVLKGV KLHYT UniProtKB: Spike glycoprotein |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 22 / 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: 8 |
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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: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 315257 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |