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- PDB-9fpz: Human NatA-MAP2 80S ribosome complex -

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Basic information

Entry
Database: PDB / ID: 9fpz
TitleHuman NatA-MAP2 80S ribosome complex
Components
  • (60S ribosomal protein ...) x 6
  • (Large ribosomal subunit protein ...) x 2
  • (N-alpha-acetyltransferase ...) x 2
  • 28S rRNA (300-MER, fragments)
  • 5.8S rRNA (58-MER)
  • Methionine aminopeptidase 2
KeywordsTRANSLATION / 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
Function and homology information


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
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 ...N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Peptidase M24A, methionine aminopeptidase, subfamily 2 / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Creatinase/aminopeptidase-like / Tetratricopeptide repeat / Acetyltransferase (GNAT) family / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / 60S ribosomal protein L19 / 60S ribosomal protein L35 / Ribosomal Protein L6, KOW domain / Ribosomal protein L6e / TPR repeat region circular profile. / 60S ribosomal protein L6E / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / TPR repeat profile. / 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 / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Tetratricopeptide repeat / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Ribosomal protein L23/L15e core domain superfamily / Translation protein SH3-like 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
: / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Methionine aminopeptidase 2 ...: / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Methionine aminopeptidase 2 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsKlein, M.A. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Multi-protein assemblies orchestrate enzymatic processing of the nascent chain on the 80S ribosome
Authors: Klein, M.A. / Wild, K. / Sinning, I.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: N-alpha-acetyltransferase 10
8: 5.8S rRNA (58-MER)
A: Methionine aminopeptidase 2
B: N-alpha-acetyltransferase 15, NatA auxiliary subunit
1: 28S rRNA (300-MER, fragments)
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,14016
Polymers465,36213
Non-polymers7783
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: Spodoptera frugiperda (fall armyworm)
References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA
#4: 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXJ9

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RNA chain , 2 types, 2 molecules 81

#2: RNA chain 5.8S rRNA (58-MER)


Mass: 18646.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#5: RNA chain 28S rRNA (300-MER, fragments)


Mass: 97089.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 1 types, 1 molecules A

#3: Protein Methionine aminopeptidase 2 / MAP 2 / MetAP 2 / Initiation factor 2-associated 67 kDa glycoprotein / p67 / p67eIF2 / Peptidase M


Mass: 53413.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase

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

#6: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#8: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#10: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#11: Protein 60S ribosomal protein L23a / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#12: Protein 60S ribosomal protein L19 / Large ribosomal subunit protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#13: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779

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

#7: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#9: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17174.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254

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Non-polymers , 2 types, 3 molecules

#14: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#15: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


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

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Details

Has ligand of interestN

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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 NatA and MAP2 bound to the PTE of the 80S ribosome
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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 41.28 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25404 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00330687
ELECTRON MICROSCOPYf_angle_d0.71943044
ELECTRON MICROSCOPYf_dihedral_angle_d20.7458408
ELECTRON MICROSCOPYf_chiral_restr0.0385027
ELECTRON MICROSCOPYf_plane_restr0.0044140

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