7wf7

Cryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to S1P

Method: ELECTRON MICROSCOPY Dmax: 125.0 Å Quality: REASONABLE

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

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–382 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) 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) scFv16 × 1 S1P (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–382; UniProt 1–382

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

Homo sapiens

UniProt P63096

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 1–354 Not recorded Sphingosine 1-phosphate receptor 1 × 1 (P21453) 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) scFv16 × 1 S1P (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 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.

573 other PDB entries and 591 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–354; UniProt 1–354

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 C; UniProt 2–340 Not recorded Sphingosine 1-phosphate receptor 1 × 1 (P21453) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) scFv16 × 1 S1P (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 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 C; PDBConstruct 7–345; UniProt 2–340

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 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 1–71 Not recorded Sphingosine 1-phosphate receptor 1 × 1 (P21453) Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) scFv16 × 1 S1P (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 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 D; 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 7wf7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7wf7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7wf7
Deposition date deposition_date2021-12-26
Structure title titleCryo-EM of Sphingosine 1-phosphate receptor 1 / Gi complex bound to S1P
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_guinier37.64
Radius of gyration Rg (electron density) rg_electron37.67
Forward intensity I(0) i0197868000.00
Molecular weight molecular_weight115830.0 kDa
Excluded volume excluded_volume146110 ų
Envelope volume envelope_volume201750 ų
Hydration-shell volume shell_volume46211 ų
Envelope diameter envelope_diameter127.0
Shell Rg shell_rg41.80
Envelope Rg envelope_rg37.46
Shape Rg shape_rg37.63
Total Rg total_rg38.07
Total atoms total_atoms8136
Residues n_residues1034
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 dmax125.0
Rg (real space) rg_real37.63
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real1.9790e+08
I(0) uncertainty (real space) i0_real_error3.2980e+06
Rg (reciprocal space) rg_reciprocal37.64
I(0) (reciprocal space) i0_reciprocal197900000.0000
Solution quality estimate total_estimate0.6650
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.7
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.589
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35520000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 0.020; Positv: 1.000; Valcen: 0.986; Smooth: 0.882

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7wf7A01
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
Domain ID domain_id7wf7C01
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_id7wf7E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7wf7E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)