[English] 日本語
Yorodumi- EMDB-31743: MERS S ectodomain trimer in complex with neutralizing antibody 11... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31743 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MERS S ectodomain trimer in complex with neutralizing antibody 111 state1 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Middle East respiratory syndrome-related coronavirus / Homo sapiens (human) / Human betacoronavirus 2c EMC/2012 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.99 Å | |||||||||
Authors | Wang X / Zhao J / Wang Z / Zeng J / Zhang S / Wang Y | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: to be published Title: MERS S ectodomain trimer in complex with neutralizing antibody 111 state1 Authors: Wang X / Zhao J / Wang Z / Zeng J / Zhang S / Wang Y | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_31743.map.gz | 12.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-31743-v30.xml emd-31743.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_31743.png | 35.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31743 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31743 | HTTPS FTP |
-Validation report
Summary document | emd_31743_validation.pdf.gz | 351 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_31743_full_validation.pdf.gz | 350.5 KB | Display | |
Data in XML | emd_31743_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_31743_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31743 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31743 | HTTPS FTP |
-Related structure data
Related structure data | 7v6nMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_31743.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.0979 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : MERS spike glycoprotein
Entire | Name: MERS spike glycoprotein |
---|---|
Components |
|
-Supramolecule #1: MERS spike glycoprotein
Supramolecule | Name: MERS spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Middle East respiratory syndrome-related coronavirus |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Supramolecule #2: MERS spike glycoprotein
Supramolecule | Name: MERS spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HKE293 |
-Supramolecule #3: antibody 111
Supramolecule | Name: antibody 111 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
---|
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human betacoronavirus 2c EMC/2012 |
Molecular weight | Theoretical: 130.718586 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ...String: YVDVGPDSVK SACIEVDIQQ TFFDKTWPRP IDVSKADGII YPQGRTYSNI TITYQGLFPY QGDHGDMYVY SAGHATGTTP QKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC G TLLRAFYC ILEPRSGNHC PAGNSYTSFA TYHTPATDCS DGNYNRNASL NSFKEYFNLR NCTFMYTYNI TEDEILEWFG IT QTAQGVH LFSSRYVDLY GGNMFQFATL PVYDTIKYYS IIPHSIRSIQ SDRKAWAAFY VYKLQPLTFL LDFSVDGYIR RAI DCGFND LSQLHCSYES FDVESGVYSV SSFEAKPSGS VVEQAEGVEC DFSPLLSGTP PQVYNFKRLV FTNCNYNLTK LLSL FSVND FTCSQISPAA IASNCYSSLI LDYFSYPLSM KSDLSVSSAG PISQFNYKQS FSNPTCLILA TVPHNLTTIT KPLKY SYIN KCSRLLSDDR TEVPQLVNAN QYSPCVSIVP STVWEDGDYY RKQLSPLEGG GWLVASGSTV AMTEQLQMGF GITVQY GTD TNSVCPKLEF ANDTKIASQL GNCVEYSLYG VSGRGVFQNC TAVGVRQQRF VYDAYQNLVG YYSDDGNYYC LRACVSV PV SVIYDKETKT HATLFGSVAC EHISSTMSQY SRSTRSMLKR RDSTYGPLQT PVGCVLGLVN SSLFVEDCKL PLGQSLCA L PDTPSTLTPR SVRSVPGEMR LASIAFNHPI QVDQLNSSYF KLSIPTNFSF GVTQEYIQTT IQKVTVDCKQ YVCNGFQKC EQLLREYGQF CSKINQALHG ANLRQDDSVR NLFASVKSSQ SSPIIPGFGG DFNLTLLEPV SISTGSRSAR SAIEDLLFDK VTIADPGYM QGYDDCMQQG PASARDLICA QYVAGYKVLP PLMDVNMEAA YTSSLLGSIA GVGWTAGLSS FAAIPFAQSI F YRLNGVGI TQQVLSENQK LIANKFNQAL GAMQTGFTTT NEAFQKVQDA VNNNAQALSK LASELSNTFG AISASIGDII QR LDVLEQD AQIDRLINGR LTTLNAFVAQ QLVRSESAAL SAQLAKDKVN ECVKAQSKRS GFCGQGTHIV SFVVNAPNGL YFM HVGYYP SNHIEVVSAY GLCDAANPTN CIAPVNGYFI KTNNTRIVDE WSYTGSSFYA PEPITSLNTK YVA |
-Macromolecule #2: 111 L
Macromolecule | Name: 111 L / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.786467 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQTPAS LSASVGDRVT ITCRASQNIS SYLNWYQQKP GKAPKVLIYD TSRLQSGVPS RFSGSASGTD FTLTISSLQP EDFATYYCQ QSCTTLRCWT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String: DIQMTQTPAS LSASVGDRVT ITCRASQNIS SYLNWYQQKP GKAPKVLIYD TSRLQSGVPS RFSGSASGTD FTLTISSLQP EDFATYYCQ QSCTTLRCWT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC |
-Macromolecule #3: 111 H
Macromolecule | Name: 111 H / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.524377 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG VVQPGRSLRL SCAASAFTFS NYGMHWVRQA PGKGLEWVAV IWSAGSLKYY ADSVKGRFII SRDNSKNTLY LQMDSLRPE DTAVYYCARE NTTYYYETSG SWGASYYFDF WGQGTLVTVS SSTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String: EVQLVESGGG VVQPGRSLRL SCAASAFTFS NYGMHWVRQA PGKGLEWVAV IWSAGSLKYY ADSVKGRFII SRDNSKNTLY LQMDSLRPE DTAVYYCARE NTTYYYETSG SWGASYYFDF WGQGTLVTVS SSTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRV |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.0 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1463548 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |