6c9m

The Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex

Method: X-RAY DIFFRACTION Dmax: 154.3 Å Quality: GOOD

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

N-alpha-acetyltransferase 15, NatA auxiliary subunit

Homo sapiens

UniProt Q9BXJ9

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 1–866 Not recorded N-alpha-acetyltransferase 10 × 1 (P41227) IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG3350, 10% Tascimate, pH 7.5, 2% acetone Resolution 2.80 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–866 Not recorded N-alpha-acetyltransferase 10 × 1 (P41227) IHP INOSITOL HEXAKISPHOSPHATE × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG3350, 10% Tascimate, pH 7.5, 2% acetone Resolution 2.80 Å R-free 0.242

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 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NAA15_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–866; UniProt 1–866 Author chain C; PDBConstruct 1–866; UniProt 1–866

N-alpha-acetyltransferase 10

Homo sapiens

UniProt P41227

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 1–235 Non-standard monomer:Yes (specific site not provided by mmCIF) N-alpha-acetyltransferase 15, NatA auxiliary subunit × 1 (Q9BXJ9) IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG3350, 10% Tascimate, pH 7.5, 2% acetone Resolution 2.80 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–235 Non-standard monomer:Yes (specific site not provided by mmCIF) N-alpha-acetyltransferase 15, NatA auxiliary subunit × 1 (Q9BXJ9) IHP INOSITOL HEXAKISPHOSPHATE × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG3350, 10% Tascimate, pH 7.5, 2% acetone Resolution 2.80 Å R-free 0.242

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 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NAA10_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–236; UniProt 1–235 Author chain D; PDBConstruct 2–236; UniProt 1–235

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 6c9m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c9m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6c9m
Deposition date deposition_date2018-01-26
Structure title titleThe Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex
Keywords keywordsNatA, N-terminal acetylation, protein complex, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.40
Radius of gyration Rg (electron density) rg_electron45.35
Forward intensity I(0) i0695285000.00
Molecular weight molecular_weight218260.0 kDa
Excluded volume excluded_volume273590 ų
Envelope volume envelope_volume385070 ų
Hydration-shell volume shell_volume71570 ų
Envelope diameter envelope_diameter161.9
Shell Rg shell_rg49.16
Envelope Rg envelope_rg44.68
Shape Rg shape_rg45.35
Total Rg total_rg45.53
Total atoms total_atoms15322
Residues n_residues1864
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 dmax154.3
Rg (real space) rg_real45.56
Rg uncertainty (real space) rg_real_error1.90
I(0) (real space) i0_real6.9530e+08
I(0) uncertainty (real space) i0_real_error1.4650e+07
Rg (reciprocal space) rg_reciprocal45.41
I(0) (reciprocal space) i0_reciprocal695200000.0000
Solution quality estimate total_estimate0.8577
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.5
Skewness Skewness skewness0.461
Kurtosis Kurtosis kurtosis-0.260
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha50490000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.793; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.792

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6c9mb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamilyd.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family familyd.108.1.0 — automated matches
Domain ID domain_idd6c9md_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamilyd.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family familyd.108.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id6c9mB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily30 — Gcn5-related N-acetyltransferase (GNAT)
Domain ID domain_id6c9mD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily30 — Gcn5-related N-acetyltransferase (GNAT)

8. Citations (1)

9. Files and Curves (10)