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Open data
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Basic information
Entry | Database: PDB / ID: 9fpz | ||||||
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Title | Human NatA-MAP2 80S ribosome complex | ||||||
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![]() | TRANSLATION / co-translational processing / ribosome associated factor (RAF) / methionine aminopeptidase 2 (MAP2) / N-terminal methionine excision (NME) / N-acetyl-transferase A (NatA) / N-termional acetylation (NTA) / UBA domain / a-solenoid / protein-protein and protein-RNA interactions | ||||||
Function / homology | ![]() negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / eukaryotic 80S initiation complex / axial mesoderm development / metalloexopeptidase activity / 90S preribosome assembly / N-acetyltransferase activity / TORC2 complex binding / middle ear morphogenesis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / internal protein amino acid acetylation / protein acetylation / metalloaminopeptidase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / chromosome organization / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / aminopeptidase activity / cytosolic ribosome / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / ossification / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / skeletal system development / positive regulation of translation / sensory perception of sound / protein processing / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to UV / ribosome binding / regulation of translation / cell body / angiogenesis / cytosolic large ribosomal subunit / transcription regulator complex / cytoplasmic translation / postsynaptic density / cell differentiation / nuclear body / protein stabilization / rRNA binding / structural constituent of ribosome / ribonucleoprotein complex / cadherin binding / translation / intracellular membrane-bounded organelle / focal adhesion / mRNA binding / synapse / dendrite / regulation of DNA-templated transcription / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å | ||||||
![]() | Klein, M.A. / Wild, K. / Sinning, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Multi-protein assemblies orchestrate enzymatic processing of the nascent chain on the 80S ribosome Authors: Klein, M.A. / Wild, K. / Sinning, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 727.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 50641MC ![]() 9fq0C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-N-alpha-acetyltransferase ... , 2 types, 2 molecules 2B
#1: Protein | Mass: 20003.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA |
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#4: Protein | Mass: 98658.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-RNA chain , 2 types, 2 molecules 81
#2: RNA chain | Mass: 18646.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: RNA chain | Mass: 97089.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 53413.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-60S ribosomal protein ... , 6 types, 6 molecules LCLkLhLXLRLr
#6: Protein | Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#8: Protein | Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Large ribosomal subunit protein ... , 2 types, 2 molecules LELY
#7: Protein | Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#9: Protein | Mass: 17174.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 3 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/IHP.gif)
#14: Chemical | #15: Chemical | ChemComp-IHP / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: human NatA and MAP2 bound to the PTE of the 80S ribosome Type: RIBOSOME / Entity ID: #1-#13 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 41.28 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.21_5207: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25404 / Symmetry type: POINT | ||||||||||||||||||||||||
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