7yk7

Cryo-EM structure of the DC591053-bound human relaxin family peptide receptor 4 (RXFP4)-Gi complex

Method: ELECTRON MICROSCOPY Dmax: 124.6 Å Quality: GOOD

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

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) Relaxin-3 receptor 2 × 1 (Q8TDU9) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) IYM [(1S)-7-ethoxy-6-methoxy-1-[2-(5-methoxy-1H-indol-3-yl)ethyl]-3,4-dihydro-1H-isoquinolin-2-yl]-morpholin-4-yl-methanone × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.75 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 1
Chains and sequence ranges Author chain G; PDBConstruct 1–71; UniProt 1–71

Guanine nucleotide-binding protein G(i) subunit alpha-2

Homo sapiens

UniProt P04899

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 I; UniProt 1–355 Mutation:S47N,G204A,E246A,A327S Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Relaxin-3 receptor 2 × 1 (Q8TDU9) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) IYM [(1S)-7-ethoxy-6-methoxy-1-[2-(5-methoxy-1H-indol-3-yl)ethyl]-3,4-dihydro-1H-isoquinolin-2-yl]-morpholin-4-yl-methanone × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.75 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.

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAI2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–355; UniProt 1–355

Relaxin-3 receptor 2

Homo sapiens

UniProt Q8TDU9

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 1–374 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) scFv16 × 1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) IYM [(1S)-7-ethoxy-6-methoxy-1-[2-(5-methoxy-1H-indol-3-yl)ethyl]-3,4-dihydro-1H-isoquinolin-2-yl]-morpholin-4-yl-methanone × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.75 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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL3R2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain R; PDBConstruct 1–374; UniProt 1–374

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 T; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63212) Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) Relaxin-3 receptor 2 × 1 (Q8TDU9) scFv16 × 1 IYM [(1S)-7-ethoxy-6-methoxy-1-[2-(5-methoxy-1H-indol-3-yl)ethyl]-3,4-dihydro-1H-isoquinolin-2-yl]-morpholin-4-yl-methanone × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.75 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 T; 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 7yk7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7yk7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7yk7
Deposition date deposition_date2022-07-21
Structure title titleCryo-EM structure of the DC591053-bound human relaxin family peptide receptor 4 (RXFP4)-Gi complex
Keywords keywordshuman relaxin family peptide receptor 4, G protein-coupled receptor, ligand recognition, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier38.06
Radius of gyration Rg (electron density) rg_electron38.19
Forward intensity I(0) i0230727000.00
Molecular weight molecular_weight124520.0 kDa
Excluded volume excluded_volume156410 ų
Envelope volume envelope_volume208780 ų
Hydration-shell volume shell_volume46982 ų
Envelope diameter envelope_diameter129.0
Shell Rg shell_rg42.43
Envelope Rg envelope_rg38.03
Shape Rg shape_rg38.19
Total Rg total_rg38.45
Total atoms total_atoms8760
Residues n_residues1122
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 dmax124.6
Rg (real space) rg_real38.02
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real2.3070e+08
I(0) uncertainty (real space) i0_real_error3.7530e+06
Rg (reciprocal space) rg_reciprocal38.05
I(0) (reciprocal space) i0_reciprocal230700000.0000
Solution quality estimate total_estimate0.8983
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.606
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38240000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.905

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7yk7S01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7yk7S02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7yk7T01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

8. Citations (1)

9. Files and Curves (10)