6xf4

Crystal structure of STING REF variant in complex with E7766

Method: X-RAY DIFFRACTION Dmax: 75.0 Å Quality: GOOD

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

Stimulator of interferon genes protein

Homo sapiens

UniProt Q86WV6

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 155–341 Chain B; UniProt 155–341 Not recorded V5V (1R,3R,15E,28R,29R,30R,31R,34R,36R,39S,41R)-29,41-difluoro-34,39-disulfanyl-2,33,35,38,40,42-hexaoxa-4,6,9,11,13,18,20,22,25,27-decaaza-34,39-diphosphaoctacyclo[28.6.4.1~3,36~.1~28,31~.0~4,8~.0~7,12~.0~19,24~.0~23,27~]dotetraconta-5,7,9,11,15,19,21,23,25-nonaene 34,39-dioxide (non-preferred name) × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;0.1M HEPES pH 7.5, 0.2M CaCl2, 15% (w/v) PEG 8000 Resolution 2.77 Å R-free 0.271

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.

84 other PDB entries and 90 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STING_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–189; UniProt 155–341 Author chain B; PDBConstruct 3–189; UniProt 155–341

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 6xf4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xf4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xf4
Deposition date deposition_date2020-06-15
Structure title titleCrystal structure of STING REF variant in complex with E7766
Keywords keywordsStimulator of interferon genes (STING), REF variant, E7766, Agonist, Macrocycle, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.72
Radius of gyration Rg (electron density) rg_electron21.57
Forward intensity I(0) i030599300.00
Molecular weight molecular_weight41485.0 kDa
Excluded volume excluded_volume51551 ų
Envelope volume envelope_volume61772 ų
Hydration-shell volume shell_volume23782 ų
Envelope diameter envelope_diameter76.1
Shell Rg shell_rg28.57
Envelope Rg envelope_rg22.03
Shape Rg shape_rg21.57
Total Rg total_rg22.45
Total atoms total_atoms2916
Residues n_residues351
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 dmax75.0
Rg (real space) rg_real22.68
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real3.0600e+07
I(0) uncertainty (real space) i0_real_error3.8190e+05
Rg (reciprocal space) rg_reciprocal22.69
I(0) (reciprocal space) i0_reciprocal30600000.0000
Solution quality estimate total_estimate0.8855
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.1
Skewness Skewness skewness0.315
Kurtosis Kurtosis kurtosis-0.387
Angular range angular_range— – 0.3500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8251000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6xf4a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.387 — STING C-terminal-like
Superfamily Superfamily superfamilyd.387.1 — STING, TM173 CTD-like
Family Family familyd.387.1.1 — Tyrosinase cofactor MelC1
Domain ID domain_idd6xf4a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6xf4b1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.387 — STING C-terminal-like
Superfamily Superfamily superfamilyd.387.1 — STING, TM173 CTD-like
Family Family familyd.387.1.1 — Tyrosinase cofactor MelC1
Domain ID domain_idd6xf4b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

8. Citations (1)

9. Files and Curves (10)