8jxs

Structure of nanobody-bound DRD1_PF-6142 complex

Method: ELECTRON MICROSCOPY Dmax: 131.4 Å Quality: GOOD

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

D(1A) dopamine receptor

Homo sapiens

UniProt P21728

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 11–362 Mutation:L112W,S325A NBA3 × 1 Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G × 1 (P0AEX9,P38507,P0A015,P06654) Fab 8D3 heavy chain × 1 Fab 8D3 light chain × 1 V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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.

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DRD1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–352; UniProt 11–362

Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Staphylococcus aureus

UniProt P06654

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 295–352 Mutation:E360Q,K363A,D364F,T367I,R368L,D404E,A405H D(1A) dopamine receptor × 1 (P21728) NBA3 × 1 Fab 8D3 heavy chain × 1 Fab 8D3 light chain × 1 V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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.

48 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPG1_STRSG
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 499–556; UniProt 295–352

Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Staphylococcus aureus

UniProt P0A015

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 103–151 Mutation:E360Q,K363A,D364F,T367I,R368L,D404E,A405H D(1A) dopamine receptor × 1 (P21728) NBA3 × 1 Fab 8D3 heavy chain × 1 Fab 8D3 light chain × 1 V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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 SPA_STAAM
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 439–487; UniProt 103–151

Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Staphylococcus aureus

UniProt P0AEX9

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 27–394 Mutation:E360Q,K363A,D364F,T367I,R368L,D404E,A405H D(1A) dopamine receptor × 1 (P21728) NBA3 × 1 Fab 8D3 heavy chain × 1 Fab 8D3 light chain × 1 V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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.

366 other PDB entries and 491 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MALE_ECOLI
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 22–389; UniProt 27–394

Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G

Staphylococcus aureus

UniProt P38507

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 289–327 Mutation:E360Q,K363A,D364F,T367I,R368L,D404E,A405H D(1A) dopamine receptor × 1 (P21728) NBA3 × 1 Fab 8D3 heavy chain × 1 Fab 8D3 light chain × 1 V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.00 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.

66 other PDB entries and 127 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPA_STAAU
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 391–429; UniProt 289–327

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 8jxs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8jxs
Deposition date deposition_date2023-07-01
Structure title titleStructure of nanobody-bound DRD1_PF-6142 complex
Keywords keywordsGPCR, DRD1, PF-6142, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier42.05
Radius of gyration Rg (electron density) rg_electron42.36
Forward intensity I(0) i0209363000.00
Molecular weight molecular_weight121820.0 kDa
Excluded volume excluded_volume153810 ų
Envelope volume envelope_volume216150 ų
Hydration-shell volume shell_volume44120 ų
Envelope diameter envelope_diameter134.5
Shell Rg shell_rg45.07
Envelope Rg envelope_rg42.10
Shape Rg shape_rg42.36
Total Rg total_rg42.49
Total atoms total_atoms8596
Residues n_residues1108
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 dmax131.4
Rg (real space) rg_real42.05
Rg uncertainty (real space) rg_real_error1.22
I(0) (real space) i0_real2.0940e+08
I(0) uncertainty (real space) i0_real_error3.6600e+06
Rg (reciprocal space) rg_reciprocal42.05
I(0) (reciprocal space) i0_reciprocal209400000.0000
Solution quality estimate total_estimate0.8759
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.6
Skewness Skewness skewness0.152
Kurtosis Kurtosis kurtosis-0.820
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16710000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.571

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)