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- PDB-8z1e: A homotrimeric GPCR architecture of the human cytomegalovirus (UL... -

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Basic information

Entry
Database: PDB / ID: 8z1e
TitleA homotrimeric GPCR architecture of the human cytomegalovirus (UL78) revealed by cryo-EM
ComponentsUncharacterized protein UL78
KeywordsANTIVIRAL PROTEIN / human cytomegalovirus (HCMV) / UL78 / homotrimeric architecture / STRUCTURAL PROTEIN
Function / homologyGPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / membrane / Uncharacterized protein UL78
Function and homology information
Biological speciesHuman cytomegalovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsChen, Y. / Li, Y. / Zhou, Q. / Cong, Z. / Lin, S. / Yan, J. / Chen, X. / Yang, D. / Ying, T. / Wang, M.-W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073904 China
CitationJournal: Cell Discov / Year: 2024
Title: A homotrimeric GPCR architecture of the human cytomegalovirus revealed by cryo-EM.
Authors: Yanyan Chen / Yang Li / Qingtong Zhou / Zhaotong Cong / Shi Lin / Jiahui Yan / Xianyue Chen / Dehua Yang / Tianlei Ying / Ming-Wei Wang /
History
DepositionApr 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein UL78
B: Uncharacterized protein UL78
R: Uncharacterized protein UL78


Theoretical massNumber of molelcules
Total (without water)95,6213
Polymers95,6213
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Uncharacterized protein UL78


Mass: 31873.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain AD169) / Gene: UL78 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16751

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A homotrimeric GPCR architecture of the human cytomegalovirus revealed by cryo-EM
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Human cytomegalovirus(strain Merlin) (HHV-5)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85264 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026678
ELECTRON MICROSCOPYf_angle_d0.3889115
ELECTRON MICROSCOPYf_dihedral_angle_d3.102915
ELECTRON MICROSCOPYf_chiral_restr0.0331103
ELECTRON MICROSCOPYf_plane_restr0.0031097

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