[English] 日本語
Yorodumi- EMDB-6703: Prefusion structure of SARS-CoV spike glycoprotein, conformation 1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6703 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Prefusion structure of SARS-CoV spike glycoprotein, conformation 1 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | SARS coronavirus BJ01 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Yuan Y / Cao D / Zhang Y / Ma J / Qi J / Wang Q / Lu G / Wu Y / Yan J / Shi Y ...Yuan Y / Cao D / Zhang Y / Ma J / Qi J / Wang Q / Lu G / Wu Y / Yan J / Shi Y / Zhang X / Gao GF | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Authors: Yuan Yuan / Duanfang Cao / Yanfang Zhang / Jun Ma / Jianxun Qi / Qihui Wang / Guangwen Lu / Ying Wu / Jinghua Yan / Yi Shi / Xinzheng Zhang / George F Gao / Abstract: The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and ...The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6703.map.gz | 28.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6703-v30.xml emd-6703.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6703_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_6703.png | 129 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6703 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6703 | HTTPS FTP |
-Validation report
Summary document | emd_6703_validation.pdf.gz | 557.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6703_full_validation.pdf.gz | 557.3 KB | Display | |
Data in XML | emd_6703_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | emd_6703_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6703 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6703 | HTTPS FTP |
-Related structure data
Related structure data | 5x58MC 6704C 6705C 6706C 6707C 5x4rC 5x4sC 5x59C 5x5bC 5x5cC 5x5fC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6703.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : SARS-CoV spike trimer
Entire | Name: SARS-CoV spike trimer |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV spike trimer
Supramolecule | Name: SARS-CoV spike trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: SARS coronavirus BJ01 / Strain: BJ01 |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: SARS coronavirus BJ01 / Strain: BJ01 |
Molecular weight | Theoretical: 136.825891 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: SDLDRCTTFD DVQAPNYTQH TSSMRGVYYP DEIFRSDTLY LTQDLFLPFY SNVTGFHTIN HTFDNPVIPF KDGIYFAATE KSNVVRGWV FGSTMNNKSQ SVIIINNSTN VVIRACNFEL CDNPFFAVSK PMGTQTHTMI FDNAFNCTFE YISDAFSLDV S EKSGNFKH ...String: SDLDRCTTFD DVQAPNYTQH TSSMRGVYYP DEIFRSDTLY LTQDLFLPFY SNVTGFHTIN HTFDNPVIPF KDGIYFAATE KSNVVRGWV FGSTMNNKSQ SVIIINNSTN VVIRACNFEL CDNPFFAVSK PMGTQTHTMI FDNAFNCTFE YISDAFSLDV S EKSGNFKH LREFVFKNKD GFLYVYKGYQ PIDVVRDLPS GFNTLKPIFK LPLGINITNF RAILTAFSPA QDTWGTSAAA YF VGYLKPT TFMLKYDENG TITDAVDCSQ NPLAELKCSV KSFEIDKGIY QTSNFRVVPS GDVVRFPNIT NLCPFGEVFN ATK FPSVYA WERKKISNCV ADYSVLYNST FFSTFKCYGV SATKLNDLCF SNVYADSFVV KGDDVRQIAP GQTGVIADYN YKLP DDFMG CVLAWNTRNI DATSTGNYNY KYRYLRHGKL RPFERDISNV PFSPDGKPCT PPALNCYWPL NDYGFYTTTG IGYQP YRVV VLSFELLNAP ATVCGPKLST DLIKNQCVNF NFNGLTGTGV LTPSSKRFQP FQQFGRDVSD FTDSVRDPKT SEILDI SPC SFGGVSVITP GTNASSEVAV LYQDVNCTDV STAIHADQLT PAWRIYSTGN NVFQTQAGCL IGAEHVDTSY ECDIPIG AG ICASYHTVSL LRSTSQKSIV AYTMSLGADS SIAYSNNTIA IPTNFSISIT TEVMPVSMAK TSVDCNMYIC GDSTECAN L LLQYGSFCTQ LNRALSGIAA EQDRNTREVF AQVKQMYKTP TLKYFGGFNF SQILPDPLKP TKRSFIEDLL FNKVTLADA GFMKQYGECL GDINARDLIC AQKFNGLTVL PPLLTDDMIA AYTAALVSGT ATAGWTFGAG AALQIPFAMQ MAYRFNGIGV TQNVLYENQ KQIANQFNKA ISQIQESLTT TSTALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDKVEAE V QIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MSFPQAAPHG VVFLHVTYVP SQ ERNFTTA PAICHEGKAY FPREGVFVFN GTSWFITQRN FFSPQIITTD NTFVSGNCDV VIGIINNTVY DPLQPELDSF KEE LDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNLNESL IDLQELGKYE QYIKIKRMKQ IEDKIEEIES KQKK IENEI ARIKKIKLVP RGSLEWSHPQ FEK |
-Macromolecule #2: N-ACETYL-D-GLUCOSAMINE
Macromolecule | Name: N-ACETYL-D-GLUCOSAMINE / type: ligand / ID: 2 / Number of copies: 42 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 8.0 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 |