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- EMDB-39724: A homotrimeric GPCR architecture of the human cytomegalovirus (UL... -

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Basic information

Entry
Database: EMDB / ID: EMD-39724
TitleA homotrimeric GPCR architecture of the human cytomegalovirus (UL78) revealed by cryo-EM
Map data
Sample
  • Complex: A homotrimeric GPCR architecture of the human cytomegalovirus revealed by cryo-EM
    • Protein or peptide: Uncharacterized protein UL78
Keywordshuman cytomegalovirus (HCMV) / UL78 / homotrimeric architecture / STRUCTURAL PROTEIN / ANTIVIRAL PROTEIN
Function / homologyGPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / membrane / Uncharacterized protein UL78
Function and homology information
Biological speciesHuman cytomegalovirus(strain Merlin) (HHV-5) / Human cytomegalovirus (strain AD169)
Methodsingle 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, 1 items
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, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39724.png

Downloads & links

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Map

FileDownload / File: emd_39724.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-1.4093099 - 2.0259163
Average (Standard dev.)-0.0003830122 (±0.04126706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39724_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39724_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A homotrimeric GPCR architecture of the human cytomegalovirus rev...

EntireName: A homotrimeric GPCR architecture of the human cytomegalovirus revealed by cryo-EM
Components
  • Complex: A homotrimeric GPCR architecture of the human cytomegalovirus revealed by cryo-EM
    • Protein or peptide: Uncharacterized protein UL78

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Supramolecule #1: A homotrimeric GPCR architecture of the human cytomegalovirus rev...

SupramoleculeName: A homotrimeric GPCR architecture of the human cytomegalovirus revealed by cryo-EM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human cytomegalovirus(strain Merlin) (HHV-5)

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Macromolecule #1: Uncharacterized protein UL78

MacromoleculeName: Uncharacterized protein UL78 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human cytomegalovirus (strain AD169)
Molecular weightTheoretical: 31.873582 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SADRAASDLL IGMFGSVSLV NLLTIIGCLW VLRVTRPPVS VMIFTWNLVL SQFFSILATM LSKGIMLRGA LNLSLCRLVL FVDDVGLYS TALFFLFLIL DRLSAISYGR DLWHHETREN AGVALYAVAF AWVLSIVAAV PTAATGSLDY RWLGCQIPIQ Y AAVDLTIK ...String:
SADRAASDLL IGMFGSVSLV NLLTIIGCLW VLRVTRPPVS VMIFTWNLVL SQFFSILATM LSKGIMLRGA LNLSLCRLVL FVDDVGLYS TALFFLFLIL DRLSAISYGR DLWHHETREN AGVALYAVAF AWVLSIVAAV PTAATGSLDY RWLGCQIPIQ Y AAVDLTIK MWFLLGAPMI AVLANVVELA YSDRRDHVWS YVGRVCTFYV TCLMLFVPYY CFRVLRGVLQ PASAAGTGFG IM DYVELAT RTLLTMRLGI LPLFIIAFFS REPTKDLDDS FDYLVERC

UniProtKB: Uncharacterized protein UL78

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85264

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