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- EMDB-8785: MERS S ectodomain trimer in complex with Fab of neutralizing anti... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8785 | |||||||||
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Title | MERS S ectodomain trimer in complex with Fab of neutralizing antibody G4 | |||||||||
![]() | MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4 | |||||||||
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Function / homology | ![]() endocytosis involved in viral entry into host cell / 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 / 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
![]() | Pallesen J / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing- ...Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing-Pui Kong / Erica L Andres / Arminja N Kettenbach / Mark R Denison / James D Chappell / Barney S Graham / Andrew B Ward / Jason S McLellan / ![]() Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. ...Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines. | |||||||||
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 | ![]() | 95.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.5 KB 24.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 77.1 KB | ||
Others | ![]() ![]() | 84.3 MB 84.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w9jMC ![]() 8783C ![]() 8784C ![]() 8786C ![]() 8787C ![]() 8788C ![]() 8789C ![]() 8790C ![]() 8791C ![]() 8792C ![]() 8793C ![]() 5vyhC ![]() 5vzrC ![]() 5w9hC ![]() 5w9iC ![]() 5w9kC ![]() 5w9lC ![]() 5w9mC ![]() 5w9nC ![]() 5w9oC ![]() 5w9pC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: MERS S ectodomain trimer in complex with variable...
File | emd_8785_half_map_1.map | ||||||||||||
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Annotation | MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: MERS S ectodomain trimer in complex with variable...
File | emd_8785_half_map_2.map | ||||||||||||
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Annotation | MERS S ectodomain trimer in complex with variable domain of neutralizing antibody G4 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : MERS S ectodomain trimer in complex with Fab of neutralizing anti...
Entire | Name: MERS S ectodomain trimer in complex with Fab of neutralizing antibody G4 |
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Components |
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-Supramolecule #1: MERS S ectodomain trimer in complex with Fab of neutralizing anti...
Supramolecule | Name: MERS S ectodomain trimer in complex with Fab of neutralizing antibody G4 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 146.325969 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT ...String: MIHSVFLLMF LLTPTESYVD VGPDSVKSAC IEVDIQQTFF DKTWPRPIDV SKADGIIYPQ GRTYSNITIT YQGLFPYQGD HGDMYVYSA GHATGTTPQK LFVANYSQDV KQFANGFVVR IGAAANSTGT VIISPSTSAT IRKIYPAFML GSSVGNFSDG K MGRFFNHT LVLLPDGCGT LLRAFYCILE PRSGNHCPAG NSYTSFATYH TPATDCSDGN YNRNASLNSF KEYFNLRNCT FM YTYNITE DEILEWFGIT QTAQGVHLFS SRYVDLYGGN MFQFATLPVY DTIKYYSIIP HSIRSIQSDR KAWAAFYVYK LQP LTFLLD FSVDGYIRRA IDCGFNDLSQ LHCSYESFDV ESGVYSVSSF EAKPSGSVVE QAEGVECDFS PLLSGTPPQV YNFK RLVFT NCNYNLTKLL SLFSVNDFTC SQISPAAIAS NCYSSLILDY FSYPLSMKSD LSVSSAGPIS QFNYKQSFSN PTCLI LATV PHNLTTITKP LKYSYINKCS RFLSDDRTEV PQLVNANQYS PCVSIVPSTV WEDGDYYRKQ LSPLEGGGWL VASGST VAM TEQLQMGFGI TVQYGTDTNS VCPKLEFAND TKIASQLGNC VEYSLYGVSG RGVFQNCTAV GVRQQRFVYD AYQNLVG YY SDDGNYYCLR ACVSVPVSVI YDKETKTHAT LFGSVACEHI SSTMSQYSRS TRSMLKRRDS TYGPLQTPVG CVLGLVNS S LFVEDCKLPL GQSLCALPDT PSTLTPASVG SVPGEMRLAS IAFNHPIQVD QLNSSYFKLS IPTNFSFGVT QEYIQTTIQ KVTVDCKQYV CNGFQKCEQL LREYGQFCSK INQALHGANL RQDDSVRNLF ASVKSSQSSP IIPGFGGDFN LTLLEPVSIS TGSRSARSA IEDLLFDKVT IADPGYMQGY DDCMQQGPAS ARDLICAQYV AGYKVLPPLM DVNMEAAYTS SLLGSIAGVG W TAGLSSFA AIPFAQSIFY RLNGVGITQQ VLSENQKLIA NKFNQALGAM QTGFTTTNEA FHKVQDAVNN NAQALSKLAS EL SNTFGAI SASIGDIIQR LDPPEQDAQI DRLINGRLTT LNAFVAQQLV RSESAALSAQ LAKDKVNECV KAQSKRSGFC GQG THIVSF VVNAPNGLYF MHVGYYPSNH IEVVSAYGLC DAANPTNCIA PVNGYFIKTN NTRIVDEWSY TGSSFYAPEP ITSL NTKYV APQVTYQNIS TNLPPPLLGN STGIDFQDEL DEFFKNVSTS IPNFGSLTQI NTTLLDLTYE MLSLQQVVKA LNESY IDLK ELGNYTYGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQ |
-Macromolecule #2: G4 VH
Macromolecule | Name: G4 VH / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.312352 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLQQSGPE LVRPGVSVKI SCKGSGYTFT DYAIHWVKQS HAKSLEWIGV FSTYYGNTNY NQKFKGRATM TVDKSSSTAY MELARLTSE DSAIYYCARK SYYVDYVDAM DYWGQGTSVT VSSASTTPPS VYPLAPGSAA QTNSMVTLGC LVKGYFPEPV T VTWNSGSL ...String: QVQLQQSGPE LVRPGVSVKI SCKGSGYTFT DYAIHWVKQS HAKSLEWIGV FSTYYGNTNY NQKFKGRATM TVDKSSSTAY MELARLTSE DSAIYYCARK SYYVDYVDAM DYWGQGTSVT VSSASTTPPS VYPLAPGSAA QTNSMVTLGC LVKGYFPEPV T VTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK IVPRDCGKGL EVLFQ |
-Macromolecule #3: G4 VL
Macromolecule | Name: G4 VL / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.867367 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFMNWF QQKPGQPPKL LISATSNQGS GVPARFIGSG SGTDFSLNIH PVEEDDTAM YFCQQSKEVP RTFGGGTKLE IKRTDAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String: DIVLTQSPAS LAVSLGQRAT ISCRASESVD NYGISFMNWF QQKPGQPPKL LISATSNQGS GVPARFIGSG SGTDFSLNIH PVEEDDTAM YFCQQSKEVP RTFGGGTKLE IKRTDAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC |
-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: 7.4 / Component - Name: TBS |
Grid | Model: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-35 / Number grids imaged: 1 / Average exposure time: 0.2 sec. / Average electron dose: 1.89 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-5w9j: |