7y12

Cryo-EM structure of MrgD-Gi complex with beta-alanine

Method: ELECTRON MICROSCOPY Dmax: 118.6 Å Quality: EXCELLENT

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

Guanine nucleotide-binding protein G(i) subunit alpha-1

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–354 Mutation:G203A, T219A, P288Q, A326S Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63213) Soluble cytochrome b562,Mas-related G-protein coupled receptor member D × 1 (P0ABE7,Q8TDS7) scFV16 × 1 BAL BETA-ALANINE × 1 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 seconds blot force 5 Resolution 3.10 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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–354; UniProt 1–354

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Mus musculus

UniProt P62874

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 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63213) Soluble cytochrome b562,Mas-related G-protein coupled receptor member D × 1 (P0ABE7,Q8TDS7) scFV16 × 1 BAL BETA-ALANINE × 1 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 seconds blot force 5 Resolution 3.10 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.

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

View Construct and Data Evidence
UniProt name GBB1_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 18–356; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Mus musculus

UniProt P63213

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 Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Soluble cytochrome b562,Mas-related G-protein coupled receptor member D × 1 (P0ABE7,Q8TDS7) scFV16 × 1 BAL BETA-ALANINE × 1 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 seconds blot force 5 Resolution 3.10 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.

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–71; UniProt 1–71

Soluble cytochrome b562,Mas-related G-protein coupled receptor member D

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 Fragment:Chimera protein of Cytochrome b-562 (UNP residues 23-127) and MrgD (UNP residues 5-321) Mutation:M29W, H124I Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63213) scFV16 × 1 BAL BETA-ALANINE × 1 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 seconds blot force 5 Resolution 3.10 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 4
Chains and sequence ranges Author chain R; PDBConstruct 25–129; UniProt 23–127

Soluble cytochrome b562,Mas-related G-protein coupled receptor member D

Homo sapiens

UniProt Q8TDS7

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 5–321 Fragment:Chimera protein of Cytochrome b-562 (UNP residues 23-127) and MrgD (UNP residues 5-321) Mutation:M29W, H124I Guanine nucleotide-binding protein G(i) subunit alpha-1 × 1 (P63096) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62874) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P63213) scFV16 × 1 BAL BETA-ALANINE × 1 PLM PALMITIC ACID × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot time 3 seconds blot force 5 Resolution 3.10 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MRGRD_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain R; PDBConstruct 130–446; UniProt 5–321

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 7y12

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7y12
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7y12
Deposition date deposition_date2022-06-06
Structure title titleCryo-EM structure of MrgD-Gi complex with beta-alanine
Keywords keywordsGPCR, Complex, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.76
Radius of gyration Rg (electron density) rg_electron36.52
Forward intensity I(0) i0218856000.00
Molecular weight molecular_weight121110.0 kDa
Excluded volume excluded_volume152190 ų
Envelope volume envelope_volume199080 ų
Hydration-shell volume shell_volume46299 ų
Envelope diameter envelope_diameter121.5
Shell Rg shell_rg41.71
Envelope Rg envelope_rg36.52
Shape Rg shape_rg36.49
Total Rg total_rg36.95
Total atoms total_atoms8501
Residues n_residues1109
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 dmax118.6
Rg (real space) rg_real36.68
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real2.1890e+08
I(0) uncertainty (real space) i0_real_error3.3580e+06
Rg (reciprocal space) rg_reciprocal36.73
I(0) (reciprocal space) i0_reciprocal218900000.0000
Solution quality estimate total_estimate0.9007
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.6
Skewness Skewness skewness0.163
Kurtosis Kurtosis kurtosis-0.631
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha34050000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.921

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7y12B01
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)