7xv3

Cryo-EM structure of LPS-bound GPR174 in complex with Gs protein

Method: ELECTRON MICROSCOPY Dmax: 125.2 Å Quality: GOOD

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

Probable G-protein coupled receptor 174

Homo sapiens

UniProt Q9BXC1

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 R; UniProt 1–333 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Engineered G protein subunit S (mini-Gs) × 1 Nb35 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GP174_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain R; PDBConstruct 1–333; UniProt 1–333

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Probable G-protein coupled receptor 174 × 1 (Q9BXC1) Engineered G protein subunit S (mini-Gs) × 1 Nb35 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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 G; PDBConstruct 1–71; UniProt 1–71

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 2–340 Not recorded Probable G-protein coupled receptor 174 × 1 (Q9BXC1) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Engineered G protein subunit S (mini-Gs) × 1 Nb35 × 1 WJS (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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 5
Chains and sequence ranges Author chain B; PDBConstruct 7–345; UniProt 2–340

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 7xv3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7xv3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7xv3
Deposition date deposition_date2022-05-20
Structure title titleCryo-EM structure of LPS-bound GPR174 in complex with Gs protein
Keywords keywordsGPCR, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.76
Radius of gyration Rg (electron density) rg_electron36.92
Forward intensity I(0) i0216141000.00
Molecular weight molecular_weight118760.0 kDa
Excluded volume excluded_volume148800 ų
Envelope volume envelope_volume204170 ų
Hydration-shell volume shell_volume47454 ų
Envelope diameter envelope_diameter129.6
Shell Rg shell_rg41.54
Envelope Rg envelope_rg36.80
Shape Rg shape_rg36.89
Total Rg total_rg37.33
Total atoms total_atoms8345
Residues n_residues1044
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 dmax125.2
Rg (real space) rg_real36.95
Rg uncertainty (real space) rg_real_error1.19
I(0) (real space) i0_real2.1610e+08
I(0) uncertainty (real space) i0_real_error4.0390e+06
Rg (reciprocal space) rg_reciprocal36.84
I(0) (reciprocal space) i0_reciprocal216100000.0000
Solution quality estimate total_estimate0.8520
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.8
Skewness Skewness skewness0.495
Kurtosis Kurtosis kurtosis-0.210
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha54750000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.902; Smooth: 0.702

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7xv3B01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id7xv3R01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins

8. Citations (1)

9. Files and Curves (10)