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2jod

Pac1-Rshort N-terminal EC domain Pacap(6-38) complex

Method: SOLUTION NMR Dmax: 57.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pituitary adenylate cyclase-activating polypeptide type I receptor

Homo sapiens

UniProt P41586

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 22–143 Fragment：residues 22-143 Pituitary adenylate cyclase-activating polypeptide × 1 （P18509） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition：0.5 mM [U-100% 13C; U-100% 15N] pac1-R N-terminal EC domain, 0.5 mM PACAP (6-38), 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 2JOD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6LPB Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein Deposited 2020-01-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 21–417（397 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6P9Y PAC1 GPCR Receptor complex Deposited 2019-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 19–468（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
7JQD Crystal Structure of PAC1r in complex with peptide antagonist Deposited 2020-08-10 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–143（126 aa） Fragment：UNP residues 18-143
Mutation：A18G, P19S, A20M, M21A, C25G, del(89-109) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 20% PEG3000, 0.2 M sodium chloride
Resolution 2.70 Å R-free 0.291
8E3X Cryo-EM structure of the PAC1R-PACAP27-Gs complex Deposited 2022-08-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 19–468（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9P92 Cryo-EM structure of the PAC1nR-VIP-Gs complex Deposited 2025-06-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 19–468（450 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9P93 Cryo-EM structure of the PAC1sR-VIP-Gs complex Deposited 2025-06-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 19–447（429 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9P94 Cryo-EM structure of the PAC1sR-PACAP27-Gs complex Deposited 2025-06-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 19–447（429 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PACR_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–106； UniProt 22–143

Pituitary adenylate cyclase-activating polypeptide

Homo sapiens

UniProt P18509

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 B； UniProt 137–169 Fragment：sequence database residues, 137-169 Pituitary adenylate cyclase-activating polypeptide type I receptor × 1 （P41586） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition：0.5 mM [U-100% 13C; U-100% 15N] pac1-R N-terminal EC domain, 0.5 mM PACAP (6-38), 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 2JOD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GEA RECEPTOR-BOUND CONFORMATION OF PACAP21 Deposited 2000-10-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 132–152（21 aa） Fragment：N-TERMINAL DOMAIN(RESIDUE 132-152)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 0.41；Pressure ambient
NMR sample composition 1.7mM PACAP21; 40mM PACAP receptor; 80mM phosphate buffer (pH 6.3) | 90% H2O/10% D2O
NMR sample composition 1.7mM PACAP21; 40mM PACAP receptor; 80mM phosphate buffer (pH 6.3) | 99.8% D2O
Resolution not provided
2D2P The solution structure of micelle-bound peptide Deposited 2005-09-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 132–169（38 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate；Pressure ambient
NMR sample composition 0.5mM PACAP38 U-15N,13C; 20mM potassium phosphate buffer; 200mM DPC; 93% H2O, 5% D2O, 2% Glycerol-1,1,2,3,3-d5 | 93% H2O, 5% D2O, 2% Glycerol-1,1,2,3,3-d5
Resolution not provided
6LPB Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein Deposited 2020-01-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 132–169（38 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6M1I CryoEM structure of human PAC1 receptor in complex with PACAP38 Deposited 2020-02-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 132–169（38 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6P9Y PAC1 GPCR Receptor complex Deposited 2019-06-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 132–169（38 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
6VN7 Cryo-EM structure of an activated VIP1 receptor-G protein complex Deposited 2020-01-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 132–158（27 aa）
Not recorded CLR CHOLESTEROL × 6 PLM PALMITIC ACID × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7VQX Cryo-EM structure of human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and Gs Deposited 2021-10-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 132–158（27 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.74 Å
7WBJ Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and Gs Deposited 2021-12-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 132–158（27 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8E3X Cryo-EM structure of the PAC1R-PACAP27-Gs complex Deposited 2022-08-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 132–158（27 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8E3Y Cryo-EM structure of the VPAC1R-PACAP27-Gs complex Deposited 2022-08-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 132–158（27 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9P94 Cryo-EM structure of the PAC1sR-PACAP27-Gs complex Deposited 2025-06-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 132–158（27 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PACA_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–33； UniProt 137–169

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 2jod

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2jod
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2jod
Deposition date deposition_date2007-03-07
Structure title titlePac1-Rshort N-terminal EC domain Pacap(6-38) complex
Keywords keywordsprotein-peptide complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.05 Å
Radius of gyration Rg (electron density) rg_electron16.02 Å
Forward intensity I(0) i05353920.00
Molecular weight molecular_weight16004.0 kDa
Excluded volume excluded_volume19735 ų
Envelope volume envelope_volume24105 ų
Hydration-shell volume shell_volume13100 ų
Envelope diameter envelope_diameter58.0 Å
Shell Rg shell_rg21.29 Å
Envelope Rg envelope_rg16.46 Å
Shape Rg shape_rg15.98 Å
Total Rg total_rg17.11 Å
Total atoms total_atoms2180
Residues n_residues139
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.9 Å
Rg (real space) rg_real17.03 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real5.3540e+06
I(0) uncertainty (real space) i0_real_error6.9120e+04
Rg (reciprocal space) rg_reciprocal17.03 Å
I(0) (reciprocal space) i0_reciprocal5354000.0000
Solution quality estimate total_estimate0.6638
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.6 Å
Skewness Skewness skewness0.291
Kurtosis Kurtosis kurtosis-0.303
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1000000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 0.379; Positv: 1.000; Valcen: 0.971; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2joda1
Class classg — Small proteins
Fold Fold foldg.76 — Hormone receptor domain
Superfamily Superfamily superfamilyg.76.1 — Hormone receptor domain
Family Family familyg.76.1.1 — Hormone receptor domain
Domain ID domain_idd2joda2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2jodb1
Class classj — Peptides
Fold Fold foldj.6 — Peptide hormones
Superfamily Superfamily superfamilyj.6.1 — Peptide hormones
Family Family familyj.6.1.1 — Peptide hormones

CATH v4.4 (1 domains)

Domain ID domain_id2jodA01
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology1240 — Hormone receptor fold
Homologous superfamily homologous superfamily10 — GPCR, family 2, extracellular hormone receptor domain
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8. Citations (1)

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9. Files and Curves (10)