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- PDB-9fq0: Human NatA-NAC-MAP1 80S ribosome complex -

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Basic information

Entry
Database: PDB / ID: 9fq0
TitleHuman NatA-NAC-MAP1 80S ribosome complex
Components
  • (60S ribosomal protein ...) x 7
  • (Large ribosomal subunit protein ...) x 2
  • (N-alpha-acetyltransferase ...) x 2
  • 28S rRNA
  • 5.8S rRNA
  • Methionine aminopeptidase 1
  • Nascent polypeptide-associated complex subunit alpha
  • Transcription factor BTF3
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 / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / NatA complex / peptide-serine-alpha-N-acetyltransferase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / regulation of skeletal muscle fiber development / negative regulation of striated muscle cell apoptotic process / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / positive regulation of skeletal muscle tissue growth / N-terminal protein amino acid acetylation / cardiac ventricle development / peptide alpha-N-acetyltransferase activity / N-terminal protein amino acid modification / peptidyl-methionine modification / skeletal muscle tissue regeneration / initiator methionyl aminopeptidase activity / heart trabecula morphogenesis / methionyl aminopeptidase / eukaryotic 80S initiation complex / translation at presynapse / axial mesoderm development / metalloexopeptidase activity / 90S preribosome assembly / N-acetyltransferase activity / TORC2 complex binding / middle ear morphogenesis / protein targeting to membrane / alpha-beta T cell differentiation / internal protein amino acid acetylation / protein acetylation / Peptide chain elongation / Selenocysteine synthesis / metalloaminopeptidase activity / 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 / protein maturation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / chromosome organization / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / aminopeptidase activity / rough endoplasmic reticulum / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / ribosomal large subunit biogenesis / skeletal system development / sensory perception of sound / wound healing / Regulation of expression of SLITs and ROBOs / platelet aggregation / cytoplasmic ribonucleoprotein granule / Inactivation, recovery and regulation of the phototransduction cascade / unfolded protein binding / protein transport / presynapse / regulation of translation / heparin binding / cell body / in utero embryonic development / cytosolic large ribosomal subunit / cytoplasmic translation / transcription coactivator activity / postsynaptic density / nuclear body / rRNA binding / structural constituent of ribosome / ribonucleoprotein complex / cadherin binding / translation / intracellular membrane-bounded organelle / focal adhesion / mRNA binding / glutamatergic synapse / synapse / dendrite / regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / N-terminal acetyltransferase A, auxiliary subunit ...Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Zinc finger C6H2-type profile. / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Metallopeptidase family M24 / Tetratricopeptide repeat / Creatinase/aminopeptidase-like / 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 L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / 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 / 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. / 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 / 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 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / N-alpha-acetyltransferase 15, NatA auxiliary subunit / Transcription factor BTF3 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 ...INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / N-alpha-acetyltransferase 15, NatA auxiliary subunit / Transcription factor BTF3 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / N-alpha-acetyltransferase 10 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL28 / Methionine aminopeptidase 1 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL6 / Nascent polypeptide-associated complex subunit alpha / Large ribosomal subunit protein uL24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.67 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
Revision 2.0Jul 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_seq_id / _em_admin.last_update ..._atom_site.label_seq_id / _em_admin.last_update / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.common_name / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
8: 5.8S rRNA
E: Methionine aminopeptidase 1
D: Transcription factor BTF3
1: 28S rRNA
LY: Large ribosomal subunit protein uL24
Lh: 60S ribosomal protein L35
LX: 60S ribosomal protein L23a
A: Nascent polypeptide-associated complex subunit alpha
LU: 60S ribosomal protein L22
LR: 60S ribosomal protein L19
Lk: 60S ribosomal protein L38
2: N-alpha-acetyltransferase 10
B: N-alpha-acetyltransferase 15, NatA auxiliary subunit
LC: 60S ribosomal protein L4
LE: Large ribosomal subunit protein eL6
Lr: 60S ribosomal protein L28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,060,56817
Polymers2,059,90816
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules 81

#1: RNA chain 5.8S rRNA


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


Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 3 types, 3 molecules EDA

#2: Protein Methionine aminopeptidase 1 / MAP 1 / MetAP 1 / Peptidase M 1


Mass: 43717.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1, KIAA0094 / Production host: Escherichia coli (E. coli) / References: UniProt: P53582, methionyl aminopeptidase
#3: Protein Transcription factor BTF3 / Nascent polypeptide-associated complex subunit beta / NAC-beta / RNA polymerase B transcription factor 3


Mass: 22201.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTF3, NACB, OK/SW-cl.8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20290
#8: Protein Nascent polypeptide-associated complex subunit alpha / NAC-alpha / Alpha-NAC


Mass: 23849.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NACA, HSD48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13765

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

#5: Protein Large ribosomal subunit protein uL24 / 60S ribosomal protein L26


Mass: 17289.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6IBH6
#15: 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

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60S ribosomal protein ... , 7 types, 7 molecules LhLXLULRLkLCLr

#6: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#7: 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
#9: Protein 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#10: 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
#11: 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
#14: 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
#16: 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
Details: SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGVEPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKN
Source: (natural) Homo sapiens (human) / References: UniProt: P46779

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

#12: 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
#13: Protein N-alpha-acetyltransferase 15, NatA auxiliary subunit


Mass: 98658.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0B4J1W3

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Non-polymers , 1 types, 1 molecules

#17: 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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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-NAC-MAP1 80S ribosome complex / Type: COMPLEX / Entity ID: #1-#16 / 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: 53.97 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24116 / Symmetry type: POINT

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