7wvv

Cryo-EM structure of the human formyl peptide receptor 2 in complex with fMLFII and Gi2

Method: ELECTRON MICROSCOPY Dmax: 116.7 Å Quality: GOOD

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

Soluble cytochrome b562,N-formyl peptide receptor 2

Homo sapiens

UniProt P0ABE7

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 23–127 Mutation:S211L FME-LEU-PHE-ILE-ILE × 1 Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 2
Chains and sequence ranges Author chain R; PDBConstruct 4–108; UniProt 23–127

Soluble cytochrome b562,N-formyl peptide receptor 2

Homo sapiens

UniProt P25090

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain R; UniProt 2–347 Mutation:S211L FME-LEU-PHE-ILE-ILE × 1 Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FPR2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain R; PDBConstruct 121–466; UniProt 2–347

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 Insufficient information Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–355 Mutation:S47N, G204A, A327S, E246A FME-LEU-PHE-ILE-ILE × 1 Soluble cytochrome b562,N-formyl peptide receptor 2 × 1 (P0ABE7,P25090) 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) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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.

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 3
Chains and sequence ranges Author chain A; PDBConstruct 1–355; UniProt 1–355

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–340 Not recorded FME-LEU-PHE-ILE-ILE × 1 Soluble cytochrome b562,N-formyl peptide receptor 2 × 1 (P0ABE7,P25090) Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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 4
Chains and sequence ranges Author chain B; PDBConstruct 13–351; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 1–71 Not recorded FME-LEU-PHE-ILE-ILE × 1 Soluble cytochrome b562,N-formyl peptide receptor 2 × 1 (P0ABE7,P25090) Guanine nucleotide-binding protein G(i) subunit alpha-2 × 1 (P04899) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 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 5
Chains and sequence ranges Author chain C; 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 7wvv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7wvv
Deposition date deposition_date2022-02-11
Structure title titleCryo-EM structure of the human formyl peptide receptor 2 in complex with fMLFII and Gi2
Keywords keywordsG protein-coupled receptor, formyl peptide receptor, FPR2, fMLFII, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.87
Radius of gyration Rg (electron density) rg_electron34.24
Forward intensity I(0) i0144707000.00
Molecular weight molecular_weight99883.0 kDa
Excluded volume excluded_volume126480 ų
Envelope volume envelope_volume159760 ų
Hydration-shell volume shell_volume40370 ų
Envelope diameter envelope_diameter124.0
Shell Rg shell_rg39.05
Envelope Rg envelope_rg34.48
Shape Rg shape_rg34.25
Total Rg total_rg34.57
Total atoms total_atoms7020
Residues n_residues910
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 dmax116.7
Rg (real space) rg_real34.01
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real1.4470e+08
I(0) uncertainty (real space) i0_real_error2.7200e+06
Rg (reciprocal space) rg_reciprocal33.92
I(0) (reciprocal space) i0_reciprocal144700000.0000
Solution quality estimate total_estimate0.8584
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.8
Skewness Skewness skewness0.473
Kurtosis Kurtosis kurtosis-0.232
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41960000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 0.874

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7wvvB01
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)