9ejc

Cryo-EM Structure of CXCL1-KSHV ORF74-Gi-scFv16 Complex

Method: ELECTRON MICROSCOPY Dmax: 144.1 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Homo sapiens

UniProt P62873

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) viral G-protein coupled receptor × 1 (Q98146) Growth-regulated alpha protein × 1 (P09341) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) scFv Recombinant Mouse Monoclonal Antibody (scFv16) × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10 mM HEPES pH 7.5, 150 mM NaCl, 0.001% (w/v) LMNG, 0.0001% (w/v) CHS, 0.001% (w/v) GDN cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 22–360; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) viral G-protein coupled receptor × 1 (Q98146) Growth-regulated alpha protein × 1 (P09341) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) scFv Recombinant Mouse Monoclonal Antibody (scFv16) × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10 mM HEPES pH 7.5, 150 mM NaCl, 0.001% (w/v) LMNG, 0.0001% (w/v) CHS, 0.001% (w/v) GDN cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 1–71

viral G-protein coupled receptor

Human gammaherpesvirus 8

UniProt Q98146

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 1–340 Mutation:G30C, L169W, L258V Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Growth-regulated alpha protein × 1 (P09341) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) scFv Recombinant Mouse Monoclonal Antibody (scFv16) × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10 mM HEPES pH 7.5, 150 mM NaCl, 0.001% (w/v) LMNG, 0.0001% (w/v) CHS, 0.001% (w/v) GDN cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGPCR_HHV8P
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–340; UniProt 1–340

Growth-regulated alpha protein

Homo sapiens

UniProt P09341

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 35–107 Mutation:N22C Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) viral G-protein coupled receptor × 1 (Q98146) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) scFv Recombinant Mouse Monoclonal Antibody (scFv16) × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10 mM HEPES pH 7.5, 150 mM NaCl, 0.001% (w/v) LMNG, 0.0001% (w/v) CHS, 0.001% (w/v) GDN cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GROA_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain F; PDBConstruct 1–73; UniProt 35–107

Guanine nucleotide-binding protein G(i) subunit alpha-1

Homo sapiens

UniProt P63096

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–354 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) viral G-protein coupled receptor × 1 (Q98146) Growth-regulated alpha protein × 1 (P09341) scFv Recombinant Mouse Monoclonal Antibody (scFv16) × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;10 mM HEPES pH 7.5, 150 mM NaCl, 0.001% (w/v) LMNG, 0.0001% (w/v) CHS, 0.001% (w/v) GDN cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.98 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

573 other PDB entries and 591 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 1–354

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9ejc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ejc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ejc
Deposition date deposition_date2024-11-27
Structure title titleCryo-EM Structure of CXCL1-KSHV ORF74-Gi-scFv16 Complex
Keywords keywords;KSHV vGPCR, Viral GPCR, KSHV ORF74, ORF74-CXCL1, ORF74 Active, CXCL1 bound ORF74, KSHV ORF74-CXCL1-Gi-scFv16, VIRAL PROTEIN, VIRAL PROTEIN-SIGNALING PROTEIN complex ;; VIRAL PROTEIN/SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.45
Radius of gyration Rg (electron density) rg_electron41.32
Forward intensity I(0) i0273232000.00
Molecular weight molecular_weight135270.0 kDa
Excluded volume excluded_volume169770 ų
Envelope volume envelope_volume236440 ų
Hydration-shell volume shell_volume49992 ų
Envelope diameter envelope_diameter152.2
Shell Rg shell_rg43.58
Envelope Rg envelope_rg42.11
Shape Rg shape_rg41.25
Total Rg total_rg41.72
Total atoms total_atoms9492
Residues n_residues1215
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax144.1
Rg (real space) rg_real41.62
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real2.7320e+08
I(0) uncertainty (real space) i0_real_error4.5050e+06
Rg (reciprocal space) rg_reciprocal41.45
I(0) (reciprocal space) i0_reciprocal273200000.0000
Solution quality estimate total_estimate0.8646
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.3
Skewness Skewness skewness0.435
Kurtosis Kurtosis kurtosis-0.277
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40710000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.815

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)