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- EMDB-31796: Local refinement of SARS-CoV-2 S-Delta variant (B.1.617.2) RBD an... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31796 | |||||||||||||||
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Title | Local refinement of SARS-CoV-2 S-Delta variant (B.1.617.2) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain | |||||||||||||||
![]() | Local refinement of SARS-CoV-2 S-Delta variant RBD and ACE2, unsharpened map | |||||||||||||||
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Function / homology | ![]() positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / Attachment and Entry / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / Maturation of spike protein / viral translation / endopeptidase activity / 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 / Potential therapeutics for SARS / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / 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 / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
![]() | Yang TJ / Yu PY / Chang YC / Hsu STD | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Local refinement of SARS-CoV-2 S-Delta variant (B.1.617.2) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain Authors: Yang TJ / Yu PY / Chang YC / Hsu STD | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 107.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
Images | ![]() | 56.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 395.5 KB | Display | ![]() |
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Full document | ![]() | 395.1 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v8bMC ![]() 7v76C ![]() 7v77C ![]() 7v78C ![]() 7v79C ![]() 7v7aC ![]() 7v7dC ![]() 7v7eC ![]() 7v7fC ![]() 7v7gC ![]() 7v7hC ![]() 7v7iC ![]() 7v7jC ![]() 7v7nC ![]() 7v7oC ![]() 7v7pC ![]() 7v7qC ![]() 7v7rC ![]() 7v7sC ![]() 7v7tC ![]() 7v7uC ![]() 7v7vC ![]() 7v7zC ![]() 7v80C ![]() 7v81C ![]() 7v82C ![]() 7v83C ![]() 7v84C ![]() 7v85C ![]() 7v86C ![]() 7v87C ![]() 7v88C ![]() 7v89C ![]() 7v8aC ![]() 7v8cC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Local refinement of SARS-CoV-2 S-Delta variant RBD and ACE2, unsharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : SARS-CoV-2 spike glycoprotein complex with Angiotensin-converting...
Entire | Name: SARS-CoV-2 spike glycoprotein complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike glycoprotein complex with Angiotensin-converting...
Supramolecule | Name: SARS-CoV-2 spike glycoprotein complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: S-Delta variant and ACE2 ectodomain fused with a C-terminal sGFP |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 540 KDa |
Recombinant expression | Organism: ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 142.047203 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MFVFLVLLPL VSSQCVNLRT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLDVYYHKNN KSWMESGVYS S ANNCTFEY ...String: MFVFLVLLPL VSSQCVNLRT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLDVYYHKNN KSWMESGVYS S ANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LL ALHRSYL TPGDSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQP TESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVI RGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYRYRLFR KSNLKPFERD ISTEIYQAGS KPCNG VEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL TGTGVLTESN KKFLPF QQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNV FQ TRAGCLIGAE HVNNSYECDI PIGAGICASY QTQTNSRGSA SSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISV T TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL NRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKDFGGFNF SQILPDPSKP SKRSFIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAG AALQIPFAMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST ASALGKLQNV VNQNAQALNT L VKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DF CGKGYHL MSFPQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFV SGNCDV VIGIVNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQE LGKYE QEFGSGGYIP EAPRDGQAYV RKDGEWVLLS TFLKGQDNSA DIQHSGRPLE SRGPFEQKLI SEEDLNMHTG HHHHH H |
-Macromolecule #2: Angiotensin-converting enzyme 2,Angiotensin-converting enzyme 2 (...
Macromolecule | Name: Angiotensin-converting enzyme 2,Angiotensin-converting enzyme 2 (ACE2) ectodomain type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 98.273477 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSSSSWLLLS LVAVTAAQST IEEQAKTFLD KFNHEAEDLF YQSSLASWNY NTNITEENVQ NMNNAGDKWS AFLKEQSTLA QMYPLQEIQ NLTVKLQLQA LQQNGSSVLS EDKSKRLNTI LNTMSTIYST GKVCNPDNPQ ECLLLEPGLN EIMANSLDYN E RLWAWESW ...String: MSSSSWLLLS LVAVTAAQST IEEQAKTFLD KFNHEAEDLF YQSSLASWNY NTNITEENVQ NMNNAGDKWS AFLKEQSTLA QMYPLQEIQ NLTVKLQLQA LQQNGSSVLS EDKSKRLNTI LNTMSTIYST GKVCNPDNPQ ECLLLEPGLN EIMANSLDYN E RLWAWESW RSEVGKQLRP LYEEYVVLKN EMARANHYED YGDYWRGDYE VNGVDGYDYS RGQLIEDVEH TFEEIKPLYE HL HAYVRAK LMNAYPSYIS PIGCLPAHLL GDMWGRFWTN LYSLTVPFGQ KPNIDVTDAM VDQAWDAQRI FKEAEKFFVS VGL PNMTQG FWENSMLTDP GNVQKAVCHP TAWDLGKGDF RILMCTKVTM DDFLTAHHEM GHIQYDMAYA AQPFLLRNGA NEGF HEAVG EIMSLSAATP KHLKSIGLLS PDFQEDNETE INFLLKQALT IVGTLPFTYM LEKWRWMVFK GEIPKDQWMK KWWEM KREI VGVVEPVPHD ETYCDPASLF HVSNDYSFIR YYTRTLYQFQ FQEALCQAAK HEGPLHKCDI SNSTEAGQKL FNMLRL GKS EPWTLALENV VGAKNMNVRP LLNYFEPLFT WLKDQNKNSF VGWSTDWSPY ADGSGGSGSG GSKGEELFTG VVPILVE LD GDVNGHKFSV RGEGEGDATN GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK RHDFFKSAMP EGYVQERT I SFKDDGTYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNFNSH NVYITADKQK NGIKANFKIR HNVEDGSVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSVL SKDPNEKRDH MVLLEFVTAA GITHGMDELY K |
-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: 3 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.6 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |