[English] 日本語
Yorodumi- EMDB-13564: Human coronavirus OC43 spike glycoprotein ectodomain in complex w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13564 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment | |||||||||
Map data | Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment | |||||||||
Sample |
| |||||||||
Keywords | Coronavirus / Glycoprotein / Antibody / Spike / VIRAL PROTEIN | |||||||||
Biological species | Human coronavirus OC43 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Hesketh EL / Townend S / Ranson NA / Hurdiss DL | |||||||||
Funding support | Netherlands, China, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes. Authors: Chunyan Wang / Emma L Hesketh / Tatiana M Shamorkina / Wentao Li / Peter J Franken / Dubravka Drabek / Rien van Haperen / Sarah Townend / Frank J M van Kuppeveld / Frank Grosveld / Neil A ...Authors: Chunyan Wang / Emma L Hesketh / Tatiana M Shamorkina / Wentao Li / Peter J Franken / Dubravka Drabek / Rien van Haperen / Sarah Townend / Frank J M van Kuppeveld / Frank Grosveld / Neil A Ranson / Joost Snijder / Raoul J de Groot / Daniel L Hurdiss / Berend-Jan Bosch / Abstract: Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus ...Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of its antigenic structure. Neutralizing antibodies are directed to the sialoglycan-receptor binding site in S1 domain, but, remarkably, also to S1. The latter block infection yet do not prevent sialoglycan binding. While two distinct neutralizing S1 epitopes are readily accessible in the prefusion S trimer, other sites are occluded such that their accessibility must be subject to conformational changes in S during cell-entry. While non-neutralizing antibodies were broadly reactive against a collection of natural OC43 variants, neutralizing antibodies generally displayed restricted binding breadth. Our data provide a structure-based understanding of protective immunity and adaptive evolution for this endemic coronavirus which emerged in humans long before SARS-CoV-2. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_13564.map.gz | 111.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-13564-v30.xml emd-13564.xml | 24 KB 24 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13564_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_13564.png | 58.2 KB | ||
Filedesc metadata | emd-13564.cif.gz | 6.6 KB | ||
Others | emd_13564_additional_1.map.gz emd_13564_half_map_1.map.gz emd_13564_half_map_2.map.gz | 99 MB 98.8 MB 98.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13564 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13564 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_13564.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Unsharpened map
File | emd_13564_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1
File | emd_13564_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_13564_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human coronavirus OC43 spike glycoprotein ectodomain in complex w...
Entire | Name: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment |
---|---|
Components |
|
-Supramolecule #1: Human coronavirus OC43 spike glycoprotein ectodomain in complex w...
Supramolecule | Name: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Human coronavirus OC43 / Strain: USA/1967 |
Molecular weight | Theoretical: 583 KDa |
-Supramolecule #2: Human coronavirus OC43 spike glycoprotein ectodomain
Supramolecule | Name: Human coronavirus OC43 spike glycoprotein ectodomain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: 37F1 antibody Fab fragment
Supramolecule | Name: 37F1 antibody Fab fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
---|
-Macromolecule #1: Human coronavirus OC43 spike glycoprotein
Macromolecule | Name: Human coronavirus OC43 spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human coronavirus OC43 / Strain: USA/1967 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMAL KGSVLLSRLW FKPPFLSDFI NGIFAKVKNT KVIKDRVMYS EFPAITIGST FVNTSYSVVV QPRTINSTQD GDNKLQGLLE ...String: MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMAL KGSVLLSRLW FKPPFLSDFI NGIFAKVKNT KVIKDRVMYS EFPAITIGST FVNTSYSVVV QPRTINSTQD GDNKLQGLLE VSVCQYNMCE YPQTICHPNL GNHRKELWHL DTGVVSCLYK RNFTYDVNAD YLYFHFYQEG GTFYAYFTDT GVVTKFLFNV YLGMALSHYY VMPLTCNSKL TLEYWVTPLT SRQYLLAFNQ DGIIFNAVDC MSDFMSEIKC KTQSIAPPTG VYELNGYTVQ PIADVYRRKP NLPNCNIEAW LNDKSVPSPL NWERKTFSNC NFNMSSLMSF IQADSFTCNN IDAAKIYGMC FSSITIDKFA IPNGRKVDLQ LGNLGYLQSF NYRIDTTATS CQLYYNLPAA NVSVSRFNPS TWNKRFGFIE DSVFKPRPAG VLTNHDVVYA QHCFKAPKNF CPCKLNGSCV GSGPGKNNGI GTCPAGTNYL TCDNLCTPDP ITFTGTYKCP QTKSLVGIGE HCSGLAVKSD YCGGNSCTCR PQAFLGWSAD SCLQGDKCNI FANFILHDVN SGLTCSTDLQ KANTDIILGV CVNYDLYGIL GQGIFVEVNA TYYNSWQNLL YDSNGNLYGF RDYITNRTFM IRSCYSGRVS AAFHANSSEP ALLFRNIKCN YVFNNSLTRQ LQPINYFDSY LGCVVNAYNS TAISVQTCDL TVGSGYCVDY SKNGGSGGAI TTGYRFTNFE PFTVNSVNDS LEPVGGLYEI QIPSEFTIGN MVEFIQTSSP KVTIDCAAFV CGDYAACKSQ LVEYGSFCDN INAILTEVNE LLDTTQLQVA NSLMNGVTLS TKLKDGVNFN VDDINFSPVL GCLGSECSKA SSRSAIEDLL FDKVKLSDVG FVEAYNNCTG GAEIRDLICV QSYKGIKVLP PLLSENQFSG YTLAATSASL FPPWTAAAGV PFYLNVQYRI NGLGVTMDVL SQNQKLIANA FNNALYAIQE GFDATNSALV KIQAVVNANA EALNNLLQQL SNRFGAISAS LQEILSRLDA LEAEAQIDRL INGRLTALNA YVSQQLSDST LVKFSAAQAM EKVNECVKSQ SSRINFCGNG NHIISLVQNA PYGLYFIHFS YVPTKYVTAR VSPGLCIAGD RGIAPKSGYF VNVNNTWMYT GSGYYYPEPI TENNVVVMST CAVNYTKAPY VMLNTSIPNL PDFKEELDQW FKNQTSVAPD LSLDYINVTF LDLLIKRMKQ IEDKIEEIES KQKKIENEIA RIKKIKLVPR GSLEWSHPQF EK |
-Macromolecule #2: 37F1 antibody heavy chain
Macromolecule | Name: 37F1 antibody heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKPSGTLSL TCAVSGGSIS STYNWWSWVR QPPGKGLEWI GEIYHSGNTN YNPSLKSRVT ISVDKSKNQF SLKLSSVTAA DTAVYYCARE DFDWLRDYYY GLDVWGQGTT VTVSS |
-Macromolecule #3: 37F1 antibody light chain
Macromolecule | Name: 37F1 antibody light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQLTQSPSF LSASVGDRVT ITCRASQGIA SFLAWYQQKP GKAPKLLIYA ASTLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYFCQQ LNSYPYTFGQ GTKLEIK |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | Purified OC43 spike ectodomain and the antibody Fab fragments were incubated together for 5 minutes at a 1:1 molar ratio |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | A 30 degree stage tilt was employed during data collection to increase the number of side views visualised due to preferential orientation. |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 759 / Average exposure time: 60.0 sec. / Average electron dose: 52.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |