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Yorodumi- EMDB-37626: Cryo-EM structure of SARS-CoV-2 prototype spike protein in comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37626 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | complex / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Hippopotamus amphibius (hippopotamus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Han P / Yang RR / Li SH | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Molecular basis of hippopotamus ACE2 binding to SARS-CoV-2 Authors: Yang R / Han P / Han P / Li D / Zhao R / Niu S / Liu K / Li S / Tian W / Gao GF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37626.map.gz | 171.1 MB | EMDB map data format | |
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Header (meta data) | emd-37626-v30.xml emd-37626.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37626_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_37626.png | 53.8 KB | ||
Filedesc metadata | emd-37626.cif.gz | 6.6 KB | ||
Others | emd_37626_half_map_1.map.gz emd_37626_half_map_2.map.gz | 318.7 MB 318.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37626 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37626 | HTTPS FTP |
-Related structure data
Related structure data | 8wloMC 8wlrC 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_37626.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_37626_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37626_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2
Entire | Name: SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2 |
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Components |
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-Supramolecule #1: SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2
Supramolecule | Name: SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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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: 135.118859 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 TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQYIKWPWY IW UniProtKB: Spike glycoprotein |
-Macromolecule #2: Angiotensin-converting enzyme
Macromolecule | Name: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Hippopotamus amphibius (hippopotamus) |
Molecular weight | Theoretical: 69.335891 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QSTTEEQAKT FLLKFDHDAE DLSYQSSLAS WNYNTNITDE NVQKMNEARA KWSAFYEEQS KAAKMFSLEE IQDLTLKRQL QALQQSGTS ALSADKSKRL NTILNTMSTI YSSGKVLDPN TQECLVLEPG LDDIMENSQD YSRRLWAWEG WRAEVGKQLR P LYEEYVVL ...String: QSTTEEQAKT FLLKFDHDAE DLSYQSSLAS WNYNTNITDE NVQKMNEARA KWSAFYEEQS KAAKMFSLEE IQDLTLKRQL QALQQSGTS ALSADKSKRL NTILNTMSTI YSSGKVLDPN TQECLVLEPG LDDIMENSQD YSRRLWAWEG WRAEVGKQLR P LYEEYVVL ENEMARANNY EDYGDYWRGD YEVTGAGDYD YSRDQLITDV ERTFAEIKPL YEQLHAYVRT KLMDAYPSHI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPSIDVTR EMENQSWDTK RIFKEAEKFF VSIGLPNMTQ GFWDNSMLTE PGD GRKVVC HPTAWDLGKG DFRIKMCTKV TMDDFLTAHH EMGHIQYDMA YATQPYLLRN GANEGFHEAV GEIMSLSAAT PHYL KALGL LPPDFYEDSE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGKIPKEQW MQKWWEMKRE IVGVVEPLPH DETYC DPAC LFHVAEDYSF IRYYTRTIYQ FQFHEALCQT AKHEGPLYKC DISNSTDAGQ RLLQMLNLGK SEPWTLALER IVGAKT MDV KPLLNYFEPL LTWLKDQNGN SFVGWSTDWT PYSE |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 25 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |