7td4

Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod

Method: ELECTRON MICROSCOPY Dmax: 118.1 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

Bos taurus

UniProt P62871

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–340 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (B2RSH2) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Sphingosine 1-phosphate receptor 1 × 1 (P21453) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 J8C 1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methyl-carbonimidoyl]-2-ethyl-phenyl]methyl]azetidine-3-carboxylic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.60 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.

72 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–340; UniProt 1–340

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

Rattus norvegicus

UniProt B2RSH2

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–354 Mutation:G203A Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Sphingosine 1-phosphate receptor 1 × 1 (P21453) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 J8C 1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methyl-carbonimidoyl]-2-ethyl-phenyl]methyl]azetidine-3-carboxylic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.60 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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 26–379; UniProt 1–354

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

Bos taurus

UniProt P63212

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 1–71 Mutation:C68S Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (B2RSH2) Sphingosine 1-phosphate receptor 1 × 1 (P21453) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 J8C 1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methyl-carbonimidoyl]-2-ethyl-phenyl]methyl]azetidine-3-carboxylic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.60 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.

215 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

Sphingosine 1-phosphate receptor 1

Homo sapiens

UniProt P21453

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain R; UniProt 2–382 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62871) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (B2RSH2) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 J8C 1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methyl-carbonimidoyl]-2-ethyl-phenyl]methyl]azetidine-3-carboxylic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.60 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.

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S1PR1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 12–392; UniProt 2–382

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 7td4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7td4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7td4
Deposition date deposition_date2021-12-30
Structure title titleSphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod
Keywords keywordsGPCR, complex, lipid, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier35.09
Radius of gyration Rg (electron density) rg_electron35.26
Forward intensity I(0) i0143100000.00
Molecular weight molecular_weight98110.0 kDa
Excluded volume excluded_volume123590 ų
Envelope volume envelope_volume158840 ų
Hydration-shell volume shell_volume38946 ų
Envelope diameter envelope_diameter127.3
Shell Rg shell_rg39.98
Envelope Rg envelope_rg35.09
Shape Rg shape_rg35.25
Total Rg total_rg35.63
Total atoms total_atoms6893
Residues n_residues894
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 dmax118.1
Rg (real space) rg_real35.26
Rg uncertainty (real space) rg_real_error1.15
I(0) (real space) i0_real1.4310e+08
I(0) uncertainty (real space) i0_real_error2.5040e+06
Rg (reciprocal space) rg_reciprocal35.16
I(0) (reciprocal space) i0_reciprocal143100000.0000
Solution quality estimate total_estimate0.8630
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.1
Skewness Skewness skewness0.443
Kurtosis Kurtosis kurtosis-0.360
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26740000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.712

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7td4B01
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_id7td4R01
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)