[English] 日本語
- PDB-6b7n: Cryo-electron microscopy structure of porcine delta coronavirus s... -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6b7n
TitleCryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state
ComponentsSpike protein
KeywordsVIRAL PROTEIN / delta coronavirus / spike / pre-fusion / cryo-EM
Function / homologyCoronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / Coronavirus S1 glycoprotein / Coronavirus S2 glycoprotein / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / integral component of membrane / Spike protein
Function and homology information
Specimen sourceDeltacoronavirus PDCoV/USA/Ohio137/2014
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsShang, J. / Zheng, Y. / Yang, Y. / Liu, C. / Geng, Q. / Tai, W. / Du, L. / Zhou, Y. / Zhang, W. / Li, F.
CitationJournal: J. Virol. / Year: 2018
Title: Cryo-Electron Microscopy Structure of Porcine Deltacoronavirus Spike Protein in the Prefusion State
Authors: Jian Shang / Yuan Zheng / Yang Yang / Chang Liu / Qibin Geng / Wanbo Tai / Lanying Du / Yusen Zhou / Wei Zhang / Fang Li
Abstract: Coronavirus spike proteins from different genera are divergent, although they all mediate coronavirus entry into cells by binding to host receptors and fusing viral and cell membranes. Here, we ...Coronavirus spike proteins from different genera are divergent, although they all mediate coronavirus entry into cells by binding to host receptors and fusing viral and cell membranes. Here, we determined the cryo-electron microscopy structure of porcine deltacoronavirus (PdCoV) spike protein at 3.3-Å resolution. The trimeric protein contains three receptor-binding S1 subunits that tightly pack into a crown-like structure and three membrane fusion S2 subunits that form a stalk. Each S1 subunit contains two domains, an N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD). PdCoV S1-NTD has the same structural fold as alpha- and betacoronavirus S1-NTDs as well as host galectins, and it recognizes sugar as its potential receptor. PdCoV S1-CTD has the same structural fold as alphacoronavirus S1-CTDs, but its structure differs from that of betacoronavirus S1-CTDs. PdCoV S1-CTD binds to an unidentified receptor on host cell surfaces. PdCoV S2 is locked in the prefusion conformation by structural restraint of S1 from a different monomeric subunit. PdCoV spike possesses several structural features that may facilitate immune evasion by the virus, such as its compact structure, concealed receptor-binding sites, and shielded critical epitopes. Overall, this study reveals that deltacoronavirus spikes are structurally and evolutionally more closely related to alphacoronavirus spikes than to betacoronavirus spikes; it also has implications for the receptor recognition, membrane fusion, and immune evasion by deltacoronaviruses as well as coronaviruses in general. IMPORTANCE In this study, we determined the cryo-electron microscopy structure of porcine deltacoronavirus (PdCoV) spike protein at a 3.3-Å resolution. This is the first atomic structure of a spike protein from the deltacoronavirus genus, which is divergent in amino acid sequences from the well-studied alpha- and betacoronavirus spike proteins. Here, we described the overall structure of the PdCoV spike and the detailed structure of each of its structural elements. Moreover, we analyzed the functions of each of the structural elements. Based on the structures and functions of these structural elements, we discussed the evolution of PdCoV spike protein in relation to the spike proteins from other coronavirus genera. This study combines the structure, function, and evolution of PdCoV spike protein and provides many insights into its receptor recognition, membrane fusion, and immune evasion.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 4, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 8, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Dec 6, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.3Jul 18, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.title / _citation.year

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7063
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: Spike protein
B: Spike protein
C: Spike protein
hetero molecules

Theoretical massNumber of molelcules
Total (without water)379,44160

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)51010
ΔGint (kcal/M)14
Surface area (Å2)113300


#1: Protein/peptide Spike protein

Mass: 122277.266 Da / Num. of mol.: 3 / Fragment: residues 18-1017
Source: (gene. exp.) Deltacoronavirus PDCoV/USA/Ohio137/2014
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A075E3D7
#2: Chemical...

Mass: 221.208 Da / Num. of mol.: 57 / Formula: C8H15NO6 / N-Acetylglucosamine

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Porcine delta coronavirus spike trimer in the pre-fusion state
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Deltacoronavirus PDCoV/USA/Ohio137/2014
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 87002 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00822704
ELECTRON MICROSCOPYf_angle_d1.17831209
ELECTRON MICROSCOPYf_dihedral_angle_d5.47413254
ELECTRON MICROSCOPYf_chiral_restr0.0654008
ELECTRON MICROSCOPYf_plane_restr0.0083912

About Yorodumi


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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


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.

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