8k4o

Cryo-EM structure of Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1

Method: ELECTRON MICROSCOPY Dmax: 147.9 Å Quality: GOOD

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

G protein-coupled receptor

Human gammaherpesvirus 8

UniProt Q76SF8

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 5–337 Not recorded Growth-regulated alpha protein × 1 (P09341) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I) subunit alpha-1 × 1 (A0A6P3VR35) Guanine nucleotide-binding protein subunit gamma × 1 (A0A663LQV7) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q76SF8_HHV8
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 1–333; UniProt 5–337

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 35–97 Not recorded G protein-coupled receptor × 1 (Q76SF8) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I) subunit alpha-1 × 1 (A0A6P3VR35) Guanine nucleotide-binding protein subunit gamma × 1 (A0A663LQV7) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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 2
Chains and sequence ranges Author chain F; PDBConstruct 1–63; UniProt 35–97

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 5–340 Not recorded G protein-coupled receptor × 1 (Q76SF8) Growth-regulated alpha protein × 1 (P09341) Guanine nucleotide-binding protein G(I) subunit alpha-1 × 1 (A0A6P3VR35) Guanine nucleotide-binding protein subunit gamma × 1 (A0A663LQV7) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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 3
Chains and sequence ranges Author chain B; PDBConstruct 1–336; UniProt 5–340

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

Homo sapiens

UniProt A0A6P3VR35

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 5–354 Not recorded G protein-coupled receptor × 1 (Q76SF8) Growth-regulated alpha protein × 1 (P09341) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein subunit gamma × 1 (A0A663LQV7) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A6P3VR35_CLUHA
Isoform
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 1–350; UniProt 5–354

Guanine nucleotide-binding protein subunit gamma

Homo sapiens

UniProt A0A663LQV7

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 9–62 Not recorded G protein-coupled receptor × 1 (Q76SF8) Growth-regulated alpha protein × 1 (P09341) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I) subunit alpha-1 × 1 (A0A6P3VR35) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A663LQV7_ATHCN
Isoform
PDB entities 5
Chains and sequence ranges Author chain G; PDBConstruct 1–54; UniProt 9–62

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 8k4o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8k4o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8k4o
Deposition date deposition_date2023-07-20
Structure title titleCryo-EM structure of Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1
Keywords keywords;Kaposi's Sarcoma Herpesvirus GPCR, KSHV-GPCR, chemokine, VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.06
Radius of gyration Rg (electron density) rg_electron41.16
Forward intensity I(0) i0192088000.00
Molecular weight molecular_weight113260.0 kDa
Excluded volume excluded_volume142300 ų
Envelope volume envelope_volume198470 ų
Hydration-shell volume shell_volume43993 ų
Envelope diameter envelope_diameter154.9
Shell Rg shell_rg41.96
Envelope Rg envelope_rg41.76
Shape Rg shape_rg41.15
Total Rg total_rg41.27
Total atoms total_atoms7946
Residues n_residues1015
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 dmax147.9
Rg (real space) rg_real41.58
Rg uncertainty (real space) rg_real_error1.61
I(0) (real space) i0_real1.9210e+08
I(0) uncertainty (real space) i0_real_error3.9000e+06
Rg (reciprocal space) rg_reciprocal41.06
I(0) (reciprocal space) i0_reciprocal192000000.0000
Solution quality estimate total_estimate0.7792
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.0
Skewness Skewness skewness0.684
Kurtosis Kurtosis kurtosis-0.077
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23860000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.595; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.705; Smooth: 0.635

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)