6pb1

Cryo-EM structure of Urocortin 1-bound Corticotropin-releasing factor 2 receptor in complex with Gs protein and Nb35

Method: ELECTRON MICROSCOPY Dmax: 136.5 Å Quality: REASONABLE

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

Corticotropin-releasing factor receptor 2

Homo sapiens

UniProt Q13324

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain P; UniProt 2–388 Not recorded Urocortin × 1 (P55089) ;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ; × 1 (P63092,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) Nanobody 35 × 1 CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRFR2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain P; PDBConstruct 1–387; UniProt 2–388

Urocortin

OrganismNot specified

UniProt P55089

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain U; UniProt 83–122 Not recorded Corticotropin-releasing factor receptor 2 × 1 (Q13324) ;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ; × 1 (P63092,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) Nanobody 35 × 1 CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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.

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UCN1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain U; PDBConstruct 1–40; UniProt 83–122

;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–67 Chain A; UniProt 206–394 Mutation:A212G, S352A Corticotropin-releasing factor receptor 2 × 1 (Q13324) Urocortin × 1 (P55089) 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 CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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 3
Chains and sequence ranges Author chain A; PDBConstruct 1–67; UniProt 1–67 Author chain A; PDBConstruct 190–378; UniProt 206–394

;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ;

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 61–182 Mutation:A212G, S352A Corticotropin-releasing factor receptor 2 × 1 (Q13324) Urocortin × 1 (P55089) 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 CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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 3
Chains and sequence ranges Author chain A; PDBConstruct 68–189; UniProt 61–182

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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded Corticotropin-releasing factor receptor 2 × 1 (Q13324) Urocortin × 1 (P55089) ;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ; × 1 (P63092,P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) Nanobody 35 × 1 CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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 4
Chains and sequence ranges Author chain B; 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 Insufficient information Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 1–71 Not recorded Corticotropin-releasing factor receptor 2 × 1 (Q13324) Urocortin × 1 (P55089) ;Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short ; × 1 (P63092,P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Nanobody 35 × 1 CLR CHOLESTEROL × 4 PLM PALMITIC ACID × 5 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 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 5
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 6pb1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6pb1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6pb1
Deposition date deposition_date2019-06-12
Structure title titleCryo-EM structure of Urocortin 1-bound Corticotropin-releasing factor 2 receptor in complex with Gs protein and Nb35
Keywords keywordsCorticotropin-releasing factor 2 receptor, urocortins1, Gs protein, GPCR, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.31
Radius of gyration Rg (electron density) rg_electron36.29
Forward intensity I(0) i0227280000.00
Molecular weight molecular_weight124780.0 kDa
Excluded volume excluded_volume157580 ų
Envelope volume envelope_volume210160 ų
Hydration-shell volume shell_volume49220 ų
Envelope diameter envelope_diameter147.3
Shell Rg shell_rg41.58
Envelope Rg envelope_rg36.55
Shape Rg shape_rg36.30
Total Rg total_rg36.65
Total atoms total_atoms8785
Residues n_residues1069
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 dmax136.5
Rg (real space) rg_real36.57
Rg uncertainty (real space) rg_real_error1.62
I(0) (real space) i0_real2.2730e+08
I(0) uncertainty (real space) i0_real_error4.1440e+06
Rg (reciprocal space) rg_reciprocal36.41
I(0) (reciprocal space) i0_reciprocal227200000.0000
Solution quality estimate total_estimate0.6016
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.2
Skewness Skewness skewness0.598
Kurtosis Kurtosis kurtosis0.061
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58670000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.587; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.773; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6pb1B00
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_id6pb1G00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain

8. Citations (1)

9. Files and Curves (10)