8j9n

Gq bound FZD1 in ligand-free state

Method: ELECTRON MICROSCOPY Dmax: 133.8 Å Quality: GOOD

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

Frizzled-1

Homo sapiens

UniProt Q9UP38

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 69–647 Not recorded Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha × 1 (P63092,P50148) 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) nanobody Nb35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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 FZD1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–579; UniProt 69–647

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha

Homo sapiens

UniProt P50148

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 28–37 Chain C; UniProt 345–359 Mutation:G49D,E50N,A249D,S252D,I372A,V375I Frizzled-1 × 1 (Q9UP38) 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) nanobody Nb35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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.

33 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAQ_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 24–33; UniProt 28–37 Author chain C; PDBConstruct 235–249; UniProt 345–359

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha

Homo sapiens

UniProt P63092

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 5–27 Chain C; UniProt 38–64 Chain C; UniProt 204–379 Mutation:G49D,E50N,A249D,S252D,I372A,V375I Frizzled-1 × 1 (Q9UP38) 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) nanobody Nb35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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.

348 other PDB entries and 356 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–23; UniProt 5–27 Author chain C; PDBConstruct 34–60; UniProt 38–64 Author chain C; PDBConstruct 69–234; UniProt 204–379

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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–340 Not recorded Frizzled-1 × 1 (Q9UP38) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha × 1 (P63092,P50148) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) nanobody Nb35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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 D; PDBConstruct 1–340; UniProt 1–340

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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 1–71 Mutation:C68S Frizzled-1 × 1 (Q9UP38) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(q) subunit alpha × 1 (P63092,P50148) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) nanobody Nb35 × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.50 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 4
Chains and sequence ranges Author chain E; PDBConstruct 1–71; UniProt 1–71

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 8j9n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8j9n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8j9n
Deposition date deposition_date2023-05-04
Structure title titleGq bound FZD1 in ligand-free state
Keywords keywordsFZD1-Gq, class-F, Frizzled receptor, Complex, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.81
Radius of gyration Rg (electron density) rg_electron39.12
Forward intensity I(0) i0222598000.00
Molecular weight molecular_weight120320.0 kDa
Excluded volume excluded_volume150250 ų
Envelope volume envelope_volume205140 ų
Hydration-shell volume shell_volume45820 ų
Envelope diameter envelope_diameter141.0
Shell Rg shell_rg42.35
Envelope Rg envelope_rg39.14
Shape Rg shape_rg39.11
Total Rg total_rg39.34
Total atoms total_atoms8469
Residues n_residues1107
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 dmax133.8
Rg (real space) rg_real39.25
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real2.2260e+08
I(0) uncertainty (real space) i0_real_error4.2050e+06
Rg (reciprocal space) rg_reciprocal38.98
I(0) (reciprocal space) i0_reciprocal222500000.0000
Solution quality estimate total_estimate0.8269
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.1
Skewness Skewness skewness0.579
Kurtosis Kurtosis kurtosis-0.206
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49490000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.858; Smooth: 0.613

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)