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Yorodumi- EMDB-22519: The N-terminus of varicella-zoster virus glycoprotein B has a fun... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22519 | |||||||||||||||||||||
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Title | The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion | |||||||||||||||||||||
Map data | Cryo-EM map of human monoclonal antibody 93k bound to varicella zoster virus glycoprotein B. | |||||||||||||||||||||
Sample |
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Function / homology | Function and homology information host cell Golgi membrane / host cell endosome membrane / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Human alphaherpesvirus 3 (Varicella-zoster virus) / unidentified (others) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||||||||||||||
Authors | Oliver SL | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: PLoS Pathog / Year: 2021 Title: The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion. Authors: Stefan L Oliver / Yi Xing / Dong-Hua Chen / Soung Hun Roh / Grigore D Pintilie / David A Bushnell / Marvin H Sommer / Edward Yang / Andrea Carfi / Wah Chiu / Ann M Arvin / Abstract: Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within ...Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within infected tissues during pathogenesis. All members of the Herpesviridae, including VZV, have a conserved core fusion complex composed of glycoproteins, gB, gH and gL. The ectodomain of the primary fusogen, gB, has five domains, DI-V, of which DI contains the fusion loops needed for fusion function. We recently demonstrated that DIV is critical for fusion initiation, which was revealed by a 2.8Å structure of a VZV neutralizing mAb, 93k, bound to gB and mutagenesis of the gB-93k interface. To further assess the mechanism of mAb 93k neutralization, the binding site of a non-neutralizing mAb to gB, SG2, was compared to mAb 93k using single particle cryogenic electron microscopy (cryo-EM). The gB-SG2 interface partially overlapped with that of gB-93k but, unlike mAb 93k, mAb SG2 did not interact with the gB N-terminus, suggesting a potential role for the gB N-terminus in membrane fusion. The gB ectodomain structure in the absence of antibody was defined at near atomic resolution by single particle cryo-EM (3.9Å) of native, full-length gB purified from infected cells and by X-ray crystallography (2.4Å) of the transiently expressed ectodomain. Both structures revealed that the VZV gB N-terminus (aa72-114) was flexible based on the absence of visible structures in the cryo-EM or X-ray crystallography data but the presence of gB N-terminal peptides were confirmed by mass spectrometry. Notably, N-terminal residues 109KSQD112 were predicted to form a small α-helix and alanine substitution of these residues abolished cell-cell fusion in a virus-free assay. Importantly, transferring the 109AAAA112 mutation into the VZV genome significantly impaired viral propagation. These data establish a functional role for the gB N-terminus in membrane fusion broadly relevant to the Herpesviridae. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22519.map.gz | 95.4 MB | EMDB map data format | |
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Header (meta data) | emd-22519-v30.xml emd-22519.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_22519.png | 90.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22519 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22519 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22519.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of human monoclonal antibody 93k bound to varicella zoster virus glycoprotein B. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.283 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Monoclonal antibody 93k bound to varicella-zoster virus glycoprotein B
Entire | Name: Monoclonal antibody 93k bound to varicella-zoster virus glycoprotein B |
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Components |
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-Supramolecule #1: Monoclonal antibody 93k bound to varicella-zoster virus glycoprotein B
Supramolecule | Name: Monoclonal antibody 93k bound to varicella-zoster virus glycoprotein B type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: varicella-zoster virus glycoprotein B
Supramolecule | Name: varicella-zoster virus glycoprotein B / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: Human alphaherpesvirus 3 (Varicella-zoster virus) |
-Supramolecule #3: monoclonal antibody 93k
Supramolecule | Name: monoclonal antibody 93k / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: unidentified (others) |
-Macromolecule #1: Monoclonal antibody 93k bound to varicella-zoster virus glycoprotein B
Macromolecule | Name: Monoclonal antibody 93k bound to varicella-zoster virus glycoprotein B type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Human alphaherpesvirus 3 (Varicella-zoster virus) |
Sequence | String: MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAVV SVSPSSFYES LQVEPTQSE DITRSAHLGD GDEIREAIHK SQDAETKPTF YVCPPPTGST IVRLEPPRTC PDYHLGKNFT EGIAVVYKEN I AAYKFKAT ...String: MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAVV SVSPSSFYES LQVEPTQSE DITRSAHLGD GDEIREAIHK SQDAETKPTF YVCPPPTGST IVRLEPPRTC PDYHLGKNFT EGIAVVYKEN I AAYKFKAT VYYKDVIVST AWAGSSYTQI TNRYADRVPI PVSEITDTID KFGKCSSKAT YVRNNHKVEA FNEDKNPQDM PL IASKYNS VGSKAWHTTN DTYMVAGTPG TYRTGTSVNC IIEEVEARSI FPYDSFGLST GDIIYMSPFF GLRDGAYREH SNY AMDRFH QFEGYRQRDL DTRALLEPAA RNFLVTPHLT VGWNWKPKRT EVCSLVKWRE VEDVVRDEYA HNFRFTMKTL STTF ISETN EFNLNQIHLS QCVKEEARAI INRIYTTRYN SSHVRTGDIQ TYLARGGFVV VFQPLLSNSL ARLYLQELVR ENTNH SPQK HPTRNTRSRR SVPVELRANR TITTTSSVEF AMLQFTYDHI QEHVNEMLAR ISSSWCQLQN RERALWSGLF PINPSA LAS TILDQRVKAR ILGDVISVSN CPELGSDTRI ILQNSMRVSG STTRCYSRPL ISIVSLNGSG TVEGQLGTDN ELIMSRD LL EPCVANHKRY FLFGHHYVYY EDYRYVREIA VHDVGMISTY VDLNLTLLKD REFMPLRVYT RDELRDTGLL DYSEIQRR N QMHSLRFYDI DKVVQYDSGT AIMQGMAQFF QGLGTAGQAV GHVVLGATGA LLSTVHGFTT FLSNPFGALA VGLLVLAGL VAAFFAYRYV LKLKTSPMKA LYPLTTKGLK QLPEGMDPFA EKPNATDTPI EEIGDSQNTE PSVNSGFDPD KFREAQEMIK YMTLVSAAE RQESKARKKN KTSALLTSRL TGLALRNRRG YSRVRTENVT GV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 7.8 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: NOT APPLICABLE |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39591 |