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Yorodumi- PDB-7rb3: Cryo-EM structure of human binary NatC complex with a Bisubstrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rb3 | ||||||
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Title | Cryo-EM structure of human binary NatC complex with a Bisubstrate inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / NatC / NAA30 / NAA35 | ||||||
Function / homology | Function and homology information N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / smooth muscle cell proliferation / Retrograde transport at the Trans-Golgi-Network / peptide alpha-N-acetyltransferase activity / negative regulation of apoptotic process / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Deng, S. / Marmorstein, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2023 Title: Molecular role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase. Authors: Sunbin Deng / Sarah M Gardner / Leah Gottlieb / Buyan Pan / E James Petersson / Ronen Marmorstein / Abstract: N-terminal acetylation occurs on over 80% of human proteins and is catalyzed by a family of N-terminal acetyltransferases (NATs). All NATs contain a small catalytic subunit, while some also contain a ...N-terminal acetylation occurs on over 80% of human proteins and is catalyzed by a family of N-terminal acetyltransferases (NATs). All NATs contain a small catalytic subunit, while some also contain a large auxiliary subunit that facilitates catalysis and ribosome targeting for co-translational acetylation. NatC is one of the major NATs containing an NAA30 catalytic subunit, but uniquely contains two auxiliary subunits, large NAA35 and small NAA38. Here, we report the cryo-EM structures of human NatC (hNatC) complexes with and without NAA38, together with biochemical studies, to reveal that NAA38 increases the thermostability and broadens the substrate-specificity profile of NatC by ordering an N-terminal segment of NAA35 and reorienting an NAA30 N-terminal peptide binding loop for optimal catalysis, respectively. We also note important differences in engagement with a stabilizing inositol hexaphosphate molecule between human and yeast NatC. These studies provide new insights for the function and evolution of the NatC complex. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rb3.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rb3.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/7rb3 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/7rb3 | HTTPS FTP |
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-Related structure data
Related structure data | 24393MC 7mx2C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 80707.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA35, EGAP, MAK10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5VZE5 |
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#2: Protein | Mass: 18083.293 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA30, C14orf35, MAK3, NAT12 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q147X3, N-terminal methionine Nalpha-acetyltransferase NatC |
#3: Chemical | ChemComp-CMC / |
#4: Chemical | ChemComp-MET / |
#5: Chemical | ChemComp-LEU / |
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
Component | Name: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm | ||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: 4222 images | ||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192437 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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