[English] 日本語
Yorodumi
- EMDB-48095: 3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48095
Title3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex
Map data3DFlex refined map of KSHV ORF74-CXCL1-Gi-scFv16 Complex
Sample
  • Complex: 3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex
    • Complex: Gi protein
    • Complex: KSHV ORF74
    • Complex: CXCL1
    • Complex: scFv16
KeywordsKSHV vGPCR / Viral GPCR / KSHV ORF74 / CXCL1-ORF74 / ORF74 Active / CXCL1 bound ORF74 / CXCL1-KSHV ORF74-Gi-scFv16 / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Human gammaherpesvirus 8 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsSahoo B / Seo HD / Dai X / Jung J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA251275 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for ligand promiscuity and high signaling activity of Kaposi's Sarcoma-associated Herpesvirus-encoded GPCR.
Authors: Jun Bae Park / Bibekananda Sahoo / Amita Rani Sahoo / Dokyun Kim / Hogyu David Seo / James Bowman / Mi-Jeong Kwak / Sophia Suh / Matthias Buck / Xinghong Dai / Jae U Jung /
Abstract: Kaposi's Sarcoma-associated Herpesvirus encodes ORF74, a viral G protein-coupled receptor homologous to CXCR2, which plays a crucial role in Kaposi's Sarcoma development through its high basal ...Kaposi's Sarcoma-associated Herpesvirus encodes ORF74, a viral G protein-coupled receptor homologous to CXCR2, which plays a crucial role in Kaposi's Sarcoma development through its high basal signaling activity. Our cryoEM analysis of ORF74 in ligand-free, BRIL-fused ligand-free, and CXCL1/Gi-bound forms elucidates its ligand-independent signaling activity. A widely open, static extracellular cavity facilitates ligand promiscuity by enabling dynamic access and diverse binding modes. Structural alterations in CWxP, E/DRY, and NPxxY micro-switches stabilize the active conformation, leading to constitutive signaling. Metadynamics simulations reveal a dynamic ensemble between local switch structures corresponding to the inactive and active states, supporting spontaneous activation. CXCR2-ORF74 chimeras highlight intracellular loops 2 and 3 as key modulators of basal and agonist-induced activity. This study defines the structural basis of ORF74's ligand promiscuity, spontaneous activation, and high basal signaling, providing insights into its role in viral oncogenesis.
History
DepositionNov 27, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48095.png

Downloads & links

-
Map

FileDownload / File: emd_48095.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3DFlex refined map of KSHV ORF74-CXCL1-Gi-scFv16 Complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 300 pix.
= 198. Å		0.66 Å/pix.
x 300 pix.
= 198. Å		0.66 Å/pix.
x 300 pix.
= 198. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.08497778 - 3.9215517
Average (Standard dev.)0.002736779 (±0.03791766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 198.00002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map B of 3DFlex refined KSHV ORF74-CXCL1-Gi-scFv16 Complex

Fileemd_48095_half_map_1.map
AnnotationHalf map B of 3DFlex refined KSHV ORF74-CXCL1-Gi-scFv16 Complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A of 3DFlex refined KSHV ORF74-CXCL1-Gi-scFv16 Complex

Fileemd_48095_half_map_2.map
AnnotationHalf map A of 3DFlex refined KSHV ORF74-CXCL1-Gi-scFv16 Complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex

EntireName: 3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex
Components
  • Complex: 3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex
    • Complex: Gi protein
    • Complex: KSHV ORF74
    • Complex: CXCL1
    • Complex: scFv16

-
Supramolecule #1: 3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex

SupramoleculeName: 3DFlex refined map of CXCL1-KSHV ORF74-Gi-scFv16 Complex
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 140 KDa

-
Supramolecule #2: Gi protein

SupramoleculeName: Gi protein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: KSHV ORF74

SupramoleculeName: KSHV ORF74 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human gammaherpesvirus 8

-
Supramolecule #4: CXCL1

SupramoleculeName: CXCL1 / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #5: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5 / Component - Concentration: 10.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES
Details: 10 mM HEPES pH 7.5, 150 mM NaCl, 0.001% (w/v) LMNG, 0.0001% (w/v) CHS, 0.001% (w/v) GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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