[English] 日本語
Yorodumi
- EMDB-22520: The N-terminus of varicella-zoster virus glycoprotein B has a fun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22520
TitleThe N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion
Map dataMonoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B.
Sample
  • Complex: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B
    • Complex: varicella-zoster virus glycoprotein B
      • Protein or peptide: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B
    • Complex: monoclonal antibody SG2
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
Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsOliver SL
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM103832 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI102546 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM079429 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI20459 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI10254601 United States
National Institutes of Health/Office of the DirectorS10-OD021600 United States
CitationJournal: 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
DepositionAug 27, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.16
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22520.png

Downloads & links

-
Map

FileDownload / File: emd_22520.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B.
Voxel sizeX=Y=Z: 2.566 Å
Density
Contour LevelBy AUTHOR: 2.16 / Movie #1: 2.16
Minimum - Maximum-7.052689 - 11.431759
Average (Standard dev.)1.0480158e-11 (±0.27297348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 513.20026 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.5662.5662.566
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z513.200513.200513.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-7.05311.4320.000

-
Supplemental data

-
Sample components

-
Entire : Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B

EntireName: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B
Components
  • Complex: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B
    • Complex: varicella-zoster virus glycoprotein B
      • Protein or peptide: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B
    • Complex: monoclonal antibody SG2

-
Supramolecule #1: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B

SupramoleculeName: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: varicella-zoster virus glycoprotein B

SupramoleculeName: varicella-zoster virus glycoprotein B / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)

-
Supramolecule #3: monoclonal antibody SG2

SupramoleculeName: monoclonal antibody SG2 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: unidentified (others)

-
Macromolecule #1: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B

MacromoleculeName: Monoclonal antibody SG2 bound to varicella-zoster virus glycoprotein B
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
SequenceString: MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAV VSVSPSSFYE SLQVEPTQSE DITRSAHLGD GDEIREAIHK SQDAETKPTF Y VCPPPTGS TIVRLEPPRT CPDYHLGKNF TEGIAVVYKE NIAAYKFKAT ...String:
MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAV VSVSPSSFYE SLQVEPTQSE DITRSAHLGD GDEIREAIHK SQDAETKPTF Y VCPPPTGS TIVRLEPPRT CPDYHLGKNF TEGIAVVYKE NIAAYKFKAT VYYKDVIVST AW AGSSYTQ ITNRYADRVP IPVSEITDTI DKFGKCSSKA TYVRNNHKVE AFNEDKNPQD MPL IASKYN SVGSKAWHTT NDTYMVAGTP GTYRTGTSVN CIIEEVEARS IFPYDSFGLS TGDI IYMSP FFGLRDGAYR EHSNYAMDRF HQFEGYRQRD LDTRALLEPA ARNFLVTPHL TVGWN WKPK RTEVCSLVKW REVEDVVRDE YAHNFRFTMK TLSTTFISET NEFNLNQIHL SQCVKE EAR AIINRIYTTR YNSSHVRTGD IQTYLARGGF VVVFQPLLSN SLARLYLQEL VRENTNH SP QKHPTRNTRS RRSVPVELRA NRTITTTSSV EFAMLQFTYD HIQEHVNEML ARISSSWC Q LQNRERALWS GLFPINPSAL ASTILDQRVK ARILGDVISV SNCPELGSDT RIILQNSMR VSGSTTRCYS RPLISIVSLN GSGTVEGQLG TDNELIMSRD LLEPCVANHK RYFLFGHHYV YYEDYRYVR EIAVHDVGMI STYVDLNLTL LKDREFMPLQ VYTRDELRDT GLLDYSEIQR R NQMHSLRF YDIDKVVQYD SGTAIMQGMA QFFQGLGTAG QAVGHVVLGA TGALLSTVHG FT TFLSNPF GALAVGLLVL AGLVAAFFAY RYVLKLKTSP MKALYPLTTK GLKQLPEGMD PFA EKPNAT DTPIEEIGDS QNTEPSVNSG FDPDKFREAQ EMIKYMTLVS AAERQESKAR KKNK TSALL TSRLTGLALR NRRGYSRVRT ENVTGV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 7.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59610

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more