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- PDB-8w1a: Cryo-EM Structure of KSHV ORF74 Apo Dimer at 2.8A -

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Basic information

Entry
Database: PDB / ID: 8w1a
TitleCryo-EM Structure of KSHV ORF74 Apo Dimer at 2.8A
Componentsviral G-protein coupled receptor
KeywordsVIRAL PROTEIN / KSHV vGPCR / Viral GPCR / KSHV ORF74 / ORF74 Apo / ORF74 Inactive
Function / homology
Function and homology information


C-C chemokine receptor activity / C-C chemokine binding / cell chemotaxis / calcium-mediated signaling / positive regulation of cytosolic calcium ion concentration / immune response / host cell plasma membrane / membrane
Similarity search - Function
: / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
viral G-protein coupled receptor
Similarity search - Component
Biological speciesHuman gammaherpesvirus 8
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsSahoo, B. / Seo, H.D. / Dai, X. / Jung, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA251275 United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of KSHV ORF74 Apo Dimer at 2.8A
Authors: Sahoo, B. / Seo, H.D. / Dai, X. / Jung, J.
History
DepositionFeb 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: viral G-protein coupled receptor
B: viral G-protein coupled receptor


Theoretical massNumber of molelcules
Total (without water)84,2652
Polymers84,2652
Non-polymers00
Water00
1
A: viral G-protein coupled receptor


Theoretical massNumber of molelcules
Total (without water)42,1321
Polymers42,1321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
B: viral G-protein coupled receptor


Theoretical massNumber of molelcules
Total (without water)42,1321
Polymers42,1321
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein viral G-protein coupled receptor / vGPCR / Protein ORF74


Mass: 42132.266 Da / Num. of mol.: 2 / Mutation: L169W, L258V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 8 / Gene: ORF74 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q98146
Has protein modificationY

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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: KSHV ORF74 (vGPCR) Apo Inverted Dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.0421 MDa / Experimental value: YES
Source (natural)Organism: Human gammaherpesvirus 8
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Details: 25 mM HEPES pH 7.5, 150 mM NaCl, 0.005% (w/v) LMNG, 0.0005% (w/v) CHS, 10% Glycerol (v/v)
Buffer componentConc.: 25 mM / Name: HPEPS / Formula: C8H18N2O4S
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 697456 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024772
ELECTRON MICROSCOPYf_angle_d0.5296502
ELECTRON MICROSCOPYf_dihedral_angle_d4.189656
ELECTRON MICROSCOPYf_chiral_restr0.035791
ELECTRON MICROSCOPYf_plane_restr0.004773

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