[English] 日本語
Yorodumi
- EMDB-7094: Glycan shield and fusion activation of a deltacoronavirus spike g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7094
TitleGlycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections
Map datadeltacoronavirus spike glycoprotein
Sample
  • Complex: Porcine deltacoronavirus spike glycoprotein
    • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / receptor-mediated virion attachment to host cell / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane
Similarity search - Function
Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike protein / Spike protein
Similarity search - Component
Biological speciesPorcine deltacoronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXiong X / Tortorici MA / Snijder S / Yoshioka C / Walls AC / Li W / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / McGuire AT / Rey FA / Bosch BJ / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM120553 United States
CitationJournal: J Virol / Year: 2018
Title: Glycan Shield and Fusion Activation of a Deltacoronavirus Spike Glycoprotein Fine-Tuned for Enteric Infections.
Authors: Xiaoli Xiong / M Alejandra Tortorici / Joost Snijder / Craig Yoshioka / Alexandra C Walls / Wentao Li / Andrew T McGuire / Félix A Rey / Berend-Jan Bosch / David Veesler /
Abstract: Coronaviruses recently emerged as major human pathogens causing outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome. They utilize the spike (S) glycoprotein anchored ...Coronaviruses recently emerged as major human pathogens causing outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome. They utilize the spike (S) glycoprotein anchored in the viral envelope to mediate host attachment and fusion of the viral and cellular membranes to initiate infection. The S protein is a major determinant of the zoonotic potential of coronaviruses and is also the main target of the host humoral immune response. We report here the 3.5-Å-resolution cryo-electron microscopy structure of the S glycoprotein trimer from the pathogenic porcine deltacoronavirus (PDCoV), which belongs to the recently identified genus. Structural and glycoproteomics data indicate that the glycans of PDCoV S are topologically conserved compared with the human respiratory coronavirus NL63 S, resulting in similar surface areas being shielded from neutralizing antibodies and implying that both viruses are under comparable immune pressure in their respective hosts. The structure further reveals a shortened S' activation loop, containing a reduced number of basic amino acids, which participates in rendering the spike largely protease resistant. This property distinguishes PDCoV S from recently characterized betacoronavirus S proteins and suggests that the S protein of enterotropic PDCoV has evolved to tolerate the protease-rich environment of the small intestine and to fine-tune its fusion activation to avoid premature triggering and reduction of infectivity. Coronaviruses use transmembrane S glycoprotein trimers to promote host attachment and fusion of the viral and cellular membranes. We determined a near-atomic-resolution cryo-electron microscopy structure of the S ectodomain trimer from the pathogenic PDCoV, which is responsible for diarrhea in piglets and has had devastating consequences for the swine industry worldwide. Structural and glycoproteomics data reveal that PDCoV S is decorated with 78 N-linked glycans obstructing the protein surface to limit accessibility to neutralizing antibodies in a way reminiscent of what has recently been described for a human respiratory coronavirus. PDCoV S is largely protease resistant, which distinguishes it from most other characterized coronavirus S glycoproteins and suggests that enteric coronaviruses have evolved to fine-tune fusion activation in the protease-rich environment of the small intestine of infected hosts.
History
DepositionOct 27, 2017-
Header (metadata) releaseNov 22, 2017-
Map releaseNov 22, 2017-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bfu
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7094.png

Downloads & links

-
Map

FileDownload / File: emd_7094.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdeltacoronavirus spike glycoprotein
Voxel sizeX=Y=Z: 1.33 Å
Density
Contour LevelBy EMDB: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.16036253 - 0.3055235
Average (Standard dev.)0.00022988567 (±0.005252281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 425.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z425.600425.600425.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1600.3060.000

-
Supplemental data

-
Sample components

-
Entire : Porcine deltacoronavirus spike glycoprotein

EntireName: Porcine deltacoronavirus spike glycoprotein
Components
  • Complex: Porcine deltacoronavirus spike glycoprotein
    • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Porcine deltacoronavirus spike glycoprotein

SupramoleculeName: Porcine deltacoronavirus spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Porcine deltacoronavirus
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)

-
Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Porcine deltacoronavirus
Molecular weightTheoretical: 112.514773 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MKLCILLAVV AFVGLSLGRS LADDLLDLLT FPGAHRFLHK PTRNSSSLYS RANNNFDVGV LPGYPTKNVN LFSPLTNSTL PINGLHRSY QPLMLNCLTK ITNHTLSMYL LPSEIQTYSC GGAMVKYQTH DAVRIILDLT ATDHISVEVV GQHGENYVFV C SEQFNYTT ...String:
MKLCILLAVV AFVGLSLGRS LADDLLDLLT FPGAHRFLHK PTRNSSSLYS RANNNFDVGV LPGYPTKNVN LFSPLTNSTL PINGLHRSY QPLMLNCLTK ITNHTLSMYL LPSEIQTYSC GGAMVKYQTH DAVRIILDLT ATDHISVEVV GQHGENYVFV C SEQFNYTT ALHNSTFFSL NSELYCFTNN TYLGILPPDL TDFTVYRTGQ FYANGYLLGT LPITVNYVRL YRGHLSANSA HF ALANLTD TLITLTNTTI SQITYCDKSV VDSIACQRSS HEVEDGFYSD PKSAVRARQR TIVTLPKLPE LEVVQLNISA HMD FGEARL DSVTINGNTS YCVTKPYFRL ETNFMCTGCT MNLRTDTCSF DLSAVNNGMS FSQFCLSTES GACEMKIIVT YVWN YLLRQ RLYVTAVEGQ THTGTTSVHA TDTSSVITDV CTDYTIYGVS GTGIIKPSDL LLHNGIAFTS PTGELYAFKN ITTGK TLQV LPCETPSQLI VINNTVVGAI TSSNSTENNR FTTTIVTPTF FYSTNATTFN CTKPVLSYGP ISVCSDGAIV GTSTLQ NTR PSIVSLYDGE VEIPSAFSLS VQTEYLQVQA EQVIVDCPQY VCNGNSRCLQ LLAQYTSACS NIEAALHSSA QLDSREI IN MFQTSTQSLQ LANITNFKGD YNFSSILTTR IGGRSAIEDL LFNKVVTSGL GTVDQDYKSC SRDMAIADLV CSQYYNGI M VLPGVVDAEK MAMYTGSLTG AMVFGGLTAA AAIPFATAVQ ARLNYVALQT NVLQENQKIL AESFNQAVGN ISLALSSVN DAIQQTSEAL NTVAIAIKKI QTVVNQQGEA LSHLTAQLSN NFQAISTSIQ DIYNRLEEVE ANQQVDRLIT GRLAALNAYV TQLLNQMSQ IRQSRLLAQQ KINECVKSQS PRYGFCGNGT HIFSLTQTAP NGIFFMHAVL VPNKFTRVNA SAGICVDNTR G YSLQPQLI LYQFNNSWRV TPRNMYEPRL PRQADFIQLT DCSVTFYNTT AANLPNIIPD IIDVNQ

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: e2initialmodel.py
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 455710

+
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