6hlt

Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of rhinovirus-14 (HRV14)

Method: X-RAY DIFFRACTION Dmax: 85.9 Å Quality: GOOD

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

Golgi resident protein GCP60

Homo sapiens

UniProt Q9H3P7

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 364–528 Not recorded Genome polyprotein × 1 (P03303) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5 Resolution 2.81 Å R-free 0.239
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 364–528 Not recorded Genome polyprotein × 1 (P03303) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5 Resolution 2.81 Å R-free 0.239

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.

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

View Construct and Data Evidence
UniProt name GCP60_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–166; UniProt 364–528 Author chain C; PDBConstruct 2–166; UniProt 364–528

Genome polyprotein

Human rhinovirus 14

UniProt P03303

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 1430–1485 Not recorded Golgi resident protein GCP60 × 1 (Q9H3P7) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5 Resolution 2.81 Å R-free 0.239
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1430–1485 Not recorded Golgi resident protein GCP60 × 1 (Q9H3P7) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5 Resolution 2.81 Å R-free 0.239

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.

58 other PDB entries and 239 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV14
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–59; UniProt 1430–1485 Author chain D; PDBConstruct 4–59; UniProt 1430–1485

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 6hlt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6hlt
Deposition date deposition_date2018-09-11
Structure title titleCrystal structure of human ACBD3 GOLD domain in complex with 3A protein of rhinovirus-14 (HRV14)
Keywords keywordscomplex, Golgi, enterovirus, picornavirus, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.86
Radius of gyration Rg (electron density) rg_electron25.46
Forward intensity I(0) i024365900.00
Molecular weight molecular_weight38826.0 kDa
Excluded volume excluded_volume48990 ų
Envelope volume envelope_volume59414 ų
Hydration-shell volume shell_volume20855 ų
Envelope diameter envelope_diameter89.6
Shell Rg shell_rg30.60
Envelope Rg envelope_rg25.72
Shape Rg shape_rg25.44
Total Rg total_rg26.17
Total atoms total_atoms2748
Residues n_residues332
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 dmax85.9
Rg (real space) rg_real26.06
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real2.4370e+07
I(0) uncertainty (real space) i0_real_error3.4530e+05
Rg (reciprocal space) rg_reciprocal26.00
I(0) (reciprocal space) i0_reciprocal24360000.0000
Solution quality estimate total_estimate0.8470
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9
Skewness Skewness skewness0.474
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4875000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.765; Smooth: 0.961

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)