3n7s

Crystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR, reveals the site of drug antagonism

Method: X-RAY DIFFRACTION Dmax: 88.0 Å Quality: GOOD

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

Calcitonin gene-related peptide type 1 receptor

Homo sapiens

UniProt Q16602

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 23–133 Fragment:UNP residues 23-133 Receptor activity-modifying protein 1 × 1 (O60894) 3N6 N-{(1S)-5-amino-1-[(4-pyridin-4-ylpiperazin-1-yl)carbonyl]pentyl}-3,5-dibromo-Nalpha-{[4-(2-oxo-1,4-dihydroquinazolin-3 (2H)-yl)piperidin-1-yl]carbonyl}-D-tyrosinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;298 K;CLR/RAMP1 complex was mixed with Olcegepant prior to crystallization in a 1:4 (protein:compound) molar ratio. Crystals were obtained by mixing 0.6uL protein with 0.3uL reservoir solution containing 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 0.4 M potassium thiocyanate. The crystals were transferred to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid nitrogen, hanging drop, temperature 298K Resolution 2.10 Å R-free 0.226
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 23–133 Fragment:UNP residues 23-133 Receptor activity-modifying protein 1 × 1 (O60894) 3N7 N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-1H-indazol-5-yl-6-methylpyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;298 K;CLR/RAMP1 complex was mixed with Olcegepant prior to crystallization in a 1:4 (protein:compound) molar ratio. Crystals were obtained by mixing 0.6uL protein with 0.3uL reservoir solution containing 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 0.4 M potassium thiocyanate. The crystals were transferred to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid nitrogen, hanging drop, temperature 298K Resolution 2.10 Å R-free 0.226

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.

24 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALRL_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–115; UniProt 23–133 Author chain B; PDBConstruct 5–115; UniProt 23–133

Receptor activity-modifying protein 1

Homo sapiens

UniProt O60894

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 26–117 Fragment:Extra-cellular domain residues 26-117 Calcitonin gene-related peptide type 1 receptor × 1 (Q16602) 3N6 N-{(1S)-5-amino-1-[(4-pyridin-4-ylpiperazin-1-yl)carbonyl]pentyl}-3,5-dibromo-Nalpha-{[4-(2-oxo-1,4-dihydroquinazolin-3 (2H)-yl)piperidin-1-yl]carbonyl}-D-tyrosinamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;298 K;CLR/RAMP1 complex was mixed with Olcegepant prior to crystallization in a 1:4 (protein:compound) molar ratio. Crystals were obtained by mixing 0.6uL protein with 0.3uL reservoir solution containing 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 0.4 M potassium thiocyanate. The crystals were transferred to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid nitrogen, hanging drop, temperature 298K Resolution 2.10 Å R-free 0.226
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 26–117 Fragment:Extra-cellular domain residues 26-117 Calcitonin gene-related peptide type 1 receptor × 1 (Q16602) 3N7 N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-1H-indazol-5-yl-6-methylpyrimidine-2,4-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;298 K;CLR/RAMP1 complex was mixed with Olcegepant prior to crystallization in a 1:4 (protein:compound) molar ratio. Crystals were obtained by mixing 0.6uL protein with 0.3uL reservoir solution containing 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 0.4 M potassium thiocyanate. The crystals were transferred to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid nitrogen, hanging drop, temperature 298K Resolution 2.10 Å R-free 0.226

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.

25 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAMP1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 5–96; UniProt 26–117 Author chain D; PDBConstruct 5–96; UniProt 26–117

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 3n7s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3n7s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3n7s
Deposition date deposition_date2010-05-27
Structure title titleCrystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR, reveals the site of drug antagonism
Keywords keywordsGPCR, class B GPCR, antagonist, olcegepant, telcagepant, migraine, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.04
Radius of gyration Rg (electron density) rg_electron24.26
Forward intensity I(0) i034850900.00
Molecular weight molecular_weight42652.0 kDa
Excluded volume excluded_volume51898 ų
Envelope volume envelope_volume65941 ų
Hydration-shell volume shell_volume23278 ų
Envelope diameter envelope_diameter91.8
Shell Rg shell_rg30.71
Envelope Rg envelope_rg24.68
Shape Rg shape_rg24.25
Total Rg total_rg25.00
Total atoms total_atoms2985
Residues n_residues364
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 dmax88.0
Rg (real space) rg_real25.10
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real3.4850e+07
I(0) uncertainty (real space) i0_real_error5.6560e+05
Rg (reciprocal space) rg_reciprocal25.08
I(0) (reciprocal space) i0_reciprocal34850000.0000
Solution quality estimate total_estimate0.8568
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.5
Skewness Skewness skewness0.402
Kurtosis Kurtosis kurtosis-0.330
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4321000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.831; Smooth: 0.980

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_id3n7sA00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology1240 — Hormone receptor fold
Homologous superfamily homologous superfamily10 — GPCR, family 2, extracellular hormone receptor domain
Domain ID domain_id3n7sB00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology1240 — Hormone receptor fold
Homologous superfamily homologous superfamily10 — GPCR, family 2, extracellular hormone receptor domain
Domain ID domain_id3n7sC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily510 — Receptor activity modifying family
Domain ID domain_id3n7sD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily510 — Receptor activity modifying family

8. Citations (1)

9. Files and Curves (10)