+Open data
-Basic information
Entry | Database: PDB / ID: 6vp9 | ||||||
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Title | Cryo-EM structure of human NatB complex | ||||||
Components |
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Keywords | TRANSFERASE / NatB / NAA20 / NAA25 | ||||||
Function / homology | Function and homology information N-terminal peptidyl-glutamine acetylation / N-terminal methionine Nalpha-acetyltransferase NatB / N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / NatB complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / Golgi apparatus / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å | ||||||
Authors | Deng, S. / Marmorstein, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: Molecular basis for N-terminal alpha-synuclein acetylation by human NatB. Authors: Sunbin Deng / Buyan Pan / Leah Gottlieb / E James Petersson / Ronen Marmorstein / Abstract: NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of ...NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vp9.cif.gz | 203.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vp9.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 6vp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vp9_validation.pdf.gz | 831.3 KB | Display | wwPDB validaton report |
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Full document | 6vp9_full_validation.pdf.gz | 861.6 KB | Display | |
Data in XML | 6vp9_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 6vp9_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/6vp9 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/6vp9 | HTTPS FTP |
-Related structure data
Related structure data | 21307MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10477 (Title: Cryo-EM structure of Human NatB with an Alpha-Synuclein peptide and CoA conjugate Data size: 2.0 TB Data #1: unaligned raw movies of hNatB with an Alpha-Synuclein peptide and CoA conjugate [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 18694.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA20, NAT5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P61599, N-terminal methionine Nalpha-acetyltransferase NatB |
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#2: Protein | Mass: 112444.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA25, C12orf30, MDM20, NAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14CX7 |
#3: Protein/peptide | Mass: 641.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) |
#4: Chemical | ChemComp-CMC / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | ||||||||||||
Electron lens | Mode: BRIGHT FIELD | ||||||||||||
Image recording |
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-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 982420 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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