8g0l

Semi-synthetic CoA-alpha-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies

Method: ELECTRON MICROSCOPY Dmax: 111.0 Å Quality: EXCELLENT

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

N-alpha-acetyltransferase 20

Homo sapiens

UniProt P61599

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–178 Not recorded N-alpha-acetyltransferase 25, NatB auxiliary subunit × 1 (Q14CX7) Alpha-synuclein × 1 (P37840) CMC CARBOXYMETHYL COENZYME *A × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.39 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 NAA20_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–178; UniProt 1–178

N-alpha-acetyltransferase 25, NatB auxiliary subunit

Homo sapiens

UniProt Q14CX7

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–972 Not recorded N-alpha-acetyltransferase 20 × 1 (P61599) Alpha-synuclein × 1 (P37840) CMC CARBOXYMETHYL COENZYME *A × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.39 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 NAA25_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–972; UniProt 1–972

Alpha-synuclein

Homo sapiens

UniProt P37840

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–5 Fragment:UNP residues 1-5 N-alpha-acetyltransferase 20 × 1 (P61599) N-alpha-acetyltransferase 25, NatB auxiliary subunit × 1 (Q14CX7) CMC CARBOXYMETHYL COENZYME *A × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.39 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.

226 other PDB entries and 234 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYUA_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–5; UniProt 1–5

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 8g0l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8g0l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8g0l
Deposition date deposition_date2023-01-31
Structure title titleSemi-synthetic CoA-alpha-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies
Keywords keywordsN-terminal acetyltransferase, TRANSFERASE; TRANSFERASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier35.26
Radius of gyration Rg (electron density) rg_electron34.55
Forward intensity I(0) i0237056000.00
Molecular weight molecular_weight126090.0 kDa
Excluded volume excluded_volume158970 ų
Envelope volume envelope_volume216370 ų
Hydration-shell volume shell_volume51585 ų
Envelope diameter envelope_diameter121.4
Shell Rg shell_rg41.79
Envelope Rg envelope_rg34.03
Shape Rg shape_rg34.52
Total Rg total_rg35.22
Total atoms total_atoms8872
Residues n_residues1088
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 dmax111.0
Rg (real space) rg_real35.11
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real2.3710e+08
I(0) uncertainty (real space) i0_real_error3.8680e+06
Rg (reciprocal space) rg_reciprocal35.20
I(0) (reciprocal space) i0_reciprocal237100000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.4
Skewness Skewness skewness0.170
Kurtosis Kurtosis kurtosis-0.507
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43660000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.943

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id8g0lB01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily1040

8. Citations (2)

9. Files and Curves (10)