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- PDB-6b7n: Cryo-electron microscopy structure of porcine delta coronavirus s... -

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Database: PDB / ID: 6b7n
TitleCryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state
DescriptorSpike protein
KeywordsVIRAL PROTEIN / delta coronavirus / spike / pre-fusion / cryo-EM
Specimen sourceDeltacoronavirus PDCoV/USA/Ohio137/2014 / virus
MethodElectron microscopy (3.3 Å resolution / Particle / Single particle)
AuthorsShang, J. / Zheng, Y. / Yang, Y. / Liu, C. / Geng, Q. / Tai, W. / Du, L. / Zhou, Y. / Zhang, W. / Li, F.
CitationJ. Virol., 2017

J. Virol., 2017 Yorodumi Papers
Cryo-EM structure of porcine delta coronavirus spike protein in the pre-fusion state.
Jian Shang / Yuan Zheng / Yang Yang / Chang Liu / Qibin Geng / Wanbo Tai / Lanying Du / Yusen Zhou / Wei Zhang / Fang Li

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

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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: Polypeptide(L)Spike protein

Mass: 122277.266 Da / Num. of mol.: 3 / Fragment: residues 18-1017
Source: (gene. exp.) Deltacoronavirus PDCoV/USA/Ohio137/2014 / virus
References: UniProt: A0A075E3D7

Cellular component

Biological process

  • fusion of virus membrane with host plasma membrane (GO: 0019064)
  • receptor-mediated virion attachment to host cell (GO: 0046813)
#2: Chemical...

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

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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
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 FIELD
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

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