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- PDB-9gj5: Human 80S ribosome in complex with NatA in distal position and Ebp1 -

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Basic information

Entry
Database: PDB / ID: 9gj5
TitleHuman 80S ribosome in complex with NatA in distal position and Ebp1
Components
  • (60S ribosomal protein ...) x 6
  • (Large ribosomal subunit protein ...) x 2
  • (N-alpha-acetyltransferase ...) x 2
  • 28S rRNA
  • 5.8S rRNA
  • Proliferation-associated protein 2G4
KeywordsTRANSLATION / human 80S ribosome / N-terminal acetylation (NTA) / N-acety-transferase A (NatA) / Ebp1 / PA2G4
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / N-acetyltransferase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / N-acetyltransferase activity / acetyltransferase activator activity / eukaryotic 80S initiation complex / regulation of translation involved in cellular response to UV / axial mesoderm development / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / protein acetylation / middle ear morphogenesis / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / chromosome organization / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-RNA complex assembly / rough endoplasmic reticulum / cytosolic ribosome / ossification / positive regulation of translation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / skeletal system development / positive regulation of cell differentiation / DNA damage response, signal transduction by p53 class mediator / sensory perception of sound / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / azurophil granule lumen / cellular response to UV / transcription corepressor activity / regulation of translation / ribosome binding / cell body / angiogenesis / transcription regulator complex / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / cell differentiation / rRNA binding / postsynaptic density / protein stabilization / nuclear body / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / ubiquitin protein ligase binding / Neutrophil degranulation / synapse / dendrite / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / endoplasmic reticulum / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Acetyltransferase (GNAT) family / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Tetratricopeptide repeat / Ribosomal protein L28e / Gcn5-related N-acetyltransferase (GNAT) domain profile. / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / GNAT domain / TPR repeat region circular profile. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L6e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / TPR repeat profile. / Ribosomal Protein L6, KOW domain / 60S ribosomal protein L35 / Acyl-CoA N-acyltransferase / 60S ribosomal protein L19 / Ribosomal protein L6e / 60S ribosomal protein L6E / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Tetratricopeptide repeats / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / Tetratricopeptide repeat / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Tetratricopeptide-like helical domain superfamily / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / Ribosomal protein L23 / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
D-chiro inositol hexakisphosphate / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 ...D-chiro inositol hexakisphosphate / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL6 / N-alpha-acetyltransferase 15, NatA auxiliary subunit / Proliferation-associated protein 2G4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.61 Å
AuthorsKlein, M.A. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: structure of human RAF complexes
Authors: Klein, M.A. / Wild, K. / Sinning, I.
History
DepositionAug 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: N-alpha-acetyltransferase 10
8: 5.8S rRNA
B: N-alpha-acetyltransferase 15, NatA auxiliary subunit
1: 28S rRNA
LC: 60S ribosomal protein L4
LE: Large ribosomal subunit protein eL6
Lk: 60S ribosomal protein L38
LY: Large ribosomal subunit protein uL24
Lh: 60S ribosomal protein L35
LX: 60S ribosomal protein L23a
LR: 60S ribosomal protein L19
Lr: 60S ribosomal protein L28
A: Proliferation-associated protein 2G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,031,39714
Polymers2,030,73713
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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N-alpha-acetyltransferase ... , 2 types, 2 molecules 2B

#1: Protein N-alpha-acetyltransferase 10 / N-terminal acetyltransferase complex ARD1 subunit homolog A / hARD1 / NatA catalytic subunit Naa10


Mass: 20003.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA10, ARD1, ARD1A, TE2 / Production host: Homo sapiens (human)
References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA
#3: Protein N-alpha-acetyltransferase 15, NatA auxiliary subunit / Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / ...Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / Protein tubedown-1 / Tbdn100


Mass: 98658.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA15, GA19, NARG1, NATH, TBDN100 / Production host: Homo sapiens (human) / References: UniProt: Q9BXJ9

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RNA chain , 2 types, 2 molecules 81

#2: RNA chain 5.8S rRNA


Mass: 50449.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: GenBank: 1142736641
#4: RNA chain 28S rRNA


Mass: 1640222.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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60S ribosomal protein ... , 6 types, 6 molecules LCLkLhLXLRLr

#5: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL4, RPL1 / Production host: Homo sapiens (human) / References: UniProt: P36578
#7: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL38 / Production host: Homo sapiens (human) / References: UniProt: P63173
#9: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14462.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL35 / Production host: Homo sapiens (human) / References: UniProt: P42766
#10: Protein 60S ribosomal protein L23a / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL23A / Production host: Homo sapiens (human) / References: UniProt: P62750
#11: Protein 60S ribosomal protein L19 / Large ribosomal subunit protein eL19


Mass: 23535.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL19 / Production host: Homo sapiens (human) / References: UniProt: P84098
#12: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL28 / Production host: Homo sapiens (human) / References: UniProt: P46779

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Large ribosomal subunit protein ... , 2 types, 2 molecules LELY

#6: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL6, TXREB1 / Production host: Homo sapiens (human) / References: UniProt: Q02878
#8: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17174.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPL26 / Production host: Homo sapiens (human) / References: UniProt: P61254

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Protein / Non-polymers , 2 types, 2 molecules A

#13: Protein Proliferation-associated protein 2G4 / Cell cycle protein p38-2G4 homolog / hG4-1 / ErbB3-binding protein 1


Mass: 43851.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PA2G4, EBP1 / Production host: Homo sapiens (human) / References: UniProt: Q9UQ80
#14: Chemical ChemComp-KGN / D-chiro inositol hexakisphosphate


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human 80S ribosome in complex with NatA and Ebp1 / Type: RIBOSOME / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 51.65 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17235 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00530707
ELECTRON MICROSCOPYf_angle_d0.86743037
ELECTRON MICROSCOPYf_dihedral_angle_d21.1348395
ELECTRON MICROSCOPYf_chiral_restr0.0475036
ELECTRON MICROSCOPYf_plane_restr0.0054134

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