8f0k

Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385

Method: ELECTRON MICROSCOPY Dmax: 158.8 Å Quality: REASONABLE

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

Receptor activity-modifying protein 3

Homo sapiens

UniProt O60896

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain E; UniProt 24–148 Not recorded San385 × 1 Calcitonin receptor × 1 (P30988) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) 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) Nanobody 35 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P42 (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate × 1 PLM PALMITIC ACID × 8 Y01 CHOLESTEROL HEMISUCCINATE × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.90 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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAMP3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 25–149; UniProt 24–148

Calcitonin receptor

Homo sapiens

UniProt P30988

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain R; UniProt 25–474 Not recorded Receptor activity-modifying protein 3 × 1 (O60896) San385 × 1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) 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) Nanobody 35 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P42 (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate × 1 PLM PALMITIC ACID × 8 Y01 CHOLESTEROL HEMISUCCINATE × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.90 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.

31 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALCR_HUMAN
Isoform P30988-2
PDB entities 3
Chains and sequence ranges Author chain R; PDBConstruct 33–482; UniProt 25–474

Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

Homo sapiens

UniProt P63092

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 1–394 Mutation:S54N, G226A, E268A, N271K, K274D, R280K, T284D, I285T Receptor activity-modifying protein 3 × 1 (O60896) San385 × 1 Calcitonin receptor × 1 (P30988) 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) Nanobody 35 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P42 (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate × 1 PLM PALMITIC ACID × 8 Y01 CHOLESTEROL HEMISUCCINATE × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.90 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.

348 other PDB entries and 356 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GNAS2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain A; PDBConstruct 1–394; UniProt 1–394

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Receptor activity-modifying protein 3 × 1 (O60896) San385 × 1 Calcitonin receptor × 1 (P30988) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody 35 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P42 (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate × 1 PLM PALMITIC ACID × 8 Y01 CHOLESTEROL HEMISUCCINATE × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.90 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 12–350; 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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Receptor activity-modifying protein 3 × 1 (O60896) San385 × 1 Calcitonin receptor × 1 (P30988) Guanine nucleotide-binding protein G(s) subunit alpha isoforms short × 1 (P63092) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Nanobody 35 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P42 (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate × 1 PLM PALMITIC ACID × 8 Y01 CHOLESTEROL HEMISUCCINATE × 2 PTY PHOSPHATIDYLETHANOLAMINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 1.90 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 6
Chains and sequence ranges Author chain G; 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 8f0k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8f0k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8f0k
Deposition date deposition_date2022-11-03
Structure title titleHuman Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
Keywords keywordsGPCR, amylin receptor, receptor activity-modifying protein, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING PROTEIN/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.45
Radius of gyration Rg (electron density) rg_electron44.26
Forward intensity I(0) i0316003000.00
Molecular weight molecular_weight149660.0 kDa
Excluded volume excluded_volume188980 ų
Envelope volume envelope_volume255140 ų
Hydration-shell volume shell_volume51410 ų
Envelope diameter envelope_diameter162.5
Shell Rg shell_rg44.93
Envelope Rg envelope_rg44.80
Shape Rg shape_rg44.24
Total Rg total_rg44.37
Total atoms total_atoms10514
Residues n_residues1272
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 dmax158.8
Rg (real space) rg_real45.10
Rg uncertainty (real space) rg_real_error1.75
I(0) (real space) i0_real3.1600e+08
I(0) uncertainty (real space) i0_real_error5.8010e+06
Rg (reciprocal space) rg_reciprocal44.46
I(0) (reciprocal space) i0_reciprocal315800000.0000
Solution quality estimate total_estimate0.7376
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.3
Skewness Skewness skewness0.610
Kurtosis Kurtosis kurtosis-0.434
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41110000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.489; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.409; Smooth: 0.708

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (13)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8f0kB01
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_id8f0kN01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)