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- EMDB-50642: Human NatA-NAC-MAP1 80S ribosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-50642
TitleHuman NatA-NAC-MAP1 80S ribosome complex
Map data
Sample
  • Complex: Human NatA-NAC-MAP1 80S ribosome complex
    • RNA: x 2 types
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
Keywordsco-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 / TRANSLATION
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 / negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / positive regulation of cell proliferation involved in heart morphogenesis / N-terminal protein amino acid acetylation / NatA complex ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / positive regulation of cell proliferation involved in heart morphogenesis / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / positive regulation of skeletal muscle tissue growth / cardiac ventricle development / protein-N-terminal amino-acid acetyltransferase activity / internal protein amino acid acetylation / N-terminal protein amino acid modification / peptidyl-methionine modification / acetyltransferase activator activity / N-acetyltransferase activity / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / heart trabecula morphogenesis / skeletal muscle tissue regeneration / eukaryotic 80S initiation complex / metalloexopeptidase activity / axial mesoderm development / 90S preribosome assembly / TORC2 complex binding / middle ear morphogenesis / alpha-beta T cell differentiation / translation at presynapse / 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 / chromosome organization / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / aminopeptidase activity / protein maturation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / cytosolic ribosome / ossification / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / skeletal system development / sensory perception of sound / wound healing / platelet aggregation / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / Inactivation, recovery and regulation of the phototransduction cascade / protein transport / regulation of translation / large ribosomal subunit / heparin binding / presynapse / ribosome binding / cell body / angiogenesis / cytosolic large ribosomal subunit / transcription regulator complex / in utero embryonic development / cytoplasmic translation / transcription coactivator activity / cell differentiation / nuclear body / protein stabilization / postsynaptic density / rRNA binding / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / intracellular membrane-bounded organelle / focal adhesion / mRNA binding / dendrite / synapse / regulation of DNA-templated transcription / negative regulation of apoptotic process / nucleolus / positive regulation of DNA-templated transcription / glutamatergic synapse / 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
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 / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Acetyltransferase (GNAT) family / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / 60S ribosomal protein L19 / Ribosomal Protein L6, KOW domain / 60S ribosomal protein L35 / 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. / Acyl-CoA N-acyltransferase / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal proteins L26 eukaryotic, L24P archaeal / 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 / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
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 ...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 / RPL26 protein / N-alpha-acetyltransferase 15, NatA auxiliary subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.67 Å
AuthorsKlein MA / Wild K / Sinning I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome.
Authors: Marius Klein / Klemens Wild / Irmgard Sinning /
Abstract: Nascent chains undergo co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine ...Nascent chains undergo co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), and N-terminal acetylation (NTA) by N-Acetyl-Transferase A (NatA), is the most common combination of subsequent modifications carried out on the 80S ribosome. How these enzymatic processes are coordinated in the context of a rapidly translating ribosome has remained elusive. Here, we report two cryo-EM structures of multi-enzyme complexes assembled on vacant human 80S ribosomes, indicating two routes for NME-NTA. Both assemblies form on the 80S independent of nascent chain substrates. Irrespective of the route, NatA occupies a non-intrusive 'distal' binding site on the ribosome which does not interfere with MAP1 or MAP2 binding nor with most other ribosome-associated factors (RAFs). NatA can partake in a coordinated, dynamic assembly with MAP1 through the hydra-like chaperoning function of the abundant Nascent Polypeptide-Associated Complex (NAC). In contrast to MAP1, MAP2 completely covers the PTE and is thus incompatible with NAC and MAP1 recruitment. Together, our data provide the structural framework for the coordinated orchestration of NME and NTA in protein biogenesis.
History
DepositionJun 14, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50642.png

Downloads & links

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Map

FileDownload / File: emd_50642.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 640 pix.
= 782.72 Å		1.22 Å/pix.
x 640 pix.
= 782.72 Å		1.22 Å/pix.
x 640 pix.
= 782.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.223 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.0509378 - 2.3178754
Average (Standard dev.)0.0001076834 (±0.092300996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 782.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50642_half_map_1.map
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Half map: #2

Fileemd_50642_half_map_2.map
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Sample components

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Entire : Human NatA-NAC-MAP1 80S ribosome complex

EntireName: Human NatA-NAC-MAP1 80S ribosome complex
Components
  • Complex: Human NatA-NAC-MAP1 80S ribosome complex
    • RNA: 5.8S rRNA
    • Protein or peptide: Methionine aminopeptidase 1
    • Protein or peptide: Transcription factor BTF3
    • RNA: 28S rRNA
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: 60S ribosomal protein L35
    • Protein or peptide: 60S ribosomal protein L23a
    • Protein or peptide: Nascent polypeptide-associated complex subunit alpha
    • Protein or peptide: 60S ribosomal protein L22
    • Protein or peptide: 60S ribosomal protein L19
    • Protein or peptide: 60S ribosomal protein L38
    • Protein or peptide: N-alpha-acetyltransferase 10
    • Protein or peptide: N-alpha-acetyltransferase 15, NatA auxiliary subunit
    • Protein or peptide: 60S ribosomal protein L4
    • Protein or peptide: Large ribosomal subunit protein eL6
    • Protein or peptide: 60S ribosomal protein L28
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: Human NatA-NAC-MAP1 80S ribosome complex

SupramoleculeName: Human NatA-NAC-MAP1 80S ribosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 5.8S rRNA

MacromoleculeName: 5.8S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.646127 KDa
SequenceString:
AACGCAGCUA GCUGCGAGAA UUAAUGUGAA UUGCAGGACA CAUUGAUCAU CGACACUU

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Macromolecule #4: 28S rRNA

MacromoleculeName: 28S rRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.640222125 MDa
SequenceString: CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC ...String:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAG AAGAAACUAA CCAGGAUUCC CUCAGUAAC GGCGAGUGAA CAGGGAAGAG CCCAGCGCCG AAUCCCCGCC CCGCGGCGGG GCGCGGGACA UGUGGCGUAC G GAAGACCC GCUCCCCGGC GCCGCUCGUG GGGGGCCCAA GUCCUUCUGA UCGAGGCCCA GCCCGUGGAC GGUGUGAGGC CG GUAGCGG CCCCCGGCGC GCCGGGCCCG GGUCUUCCCG GAGUCGGGUU GCUUGGGAAU GCAGCCCAAA GCGGGUGGUA AAC UCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAAGGGA AAGUUGAAAA GAACUUUGAA GAGA GAGUU CAAGAGGGCG UGAAACCGUU AAGAGGUAAA CGGGUGGGGU CCGCGCAGUC CGCCCGGAGG AUUCAACCCG GCGGC GGGU CCGGCCGUGU CGGCGGCCCG GCGGAUCUUU CCCGCCCCCC GUUCCUCCCG ACCCCUCCAC CCGCCCUCCC UUCCCC CGC CGCCCCUCCU CCUCCUCCCC GGAGGGGGCG GGCUCCGGCG GGUGCGGGGG UGGGCGGGCG GGGCCGGGGG UGGGGUC GG CGGGGGACCG UCCCCCGACC GGCGACCGGC CGCCGCCGGG CGCAUUUCCA CCGCGGCGGU GCGCCGCGAC CGGCUCCG G GACGGCUGGG AAGGCCCGGC GGGGAAGGUG GCUCGGGGGG CCCCGUCCGU CCGUCCGUCC GUCCUCCUCC UCCCCCGUC UCCGCCCCCC GGCCCCGCGU CCUCCCUCGG GAGGGCGCGC GGGUCGGGGC GGCGGCGGCG GCGGCGGUGG CGGCGGCGGC GGCGGCGGC GGGACCGAAA CCCCCCCCGA GUGUUACAGC CCCCCCGGCA GCAGCACUCG CCGAAUCCCG GGGCCGAGGG A GCGAGACC CGUCGCCGCG CUCUCCCCCC UCCCGGCGCC CACCCCCGCG GGGAAUCCCC CGCGAGGGGG GUCUCCCCCG CG GGGGCGC GCCGGCGUCU CCUCGUGGGG GGGCCGGGCC ACCCCUCCCA CGGCGCGACC GCUCUCCCAC CCCUCCUCCC CGC GCCCCC GCCCCGGCGA CGGGGGGGGU GCCGCGCGCG GGUCGGGGGG CGGGGCGGAC UGUCCCCAGU GCGCCCCGGG CGGG UCGCG CCGUCGGGCC CGGGGGAGGU UCUCUCGGGG CCACGCGCGC GUCCCCCGAA GAGGGGGACG GCGGAGCGAG CGCAC GGGG UCGGCGGCGA CGUCGGCUAC CCACCCGACC CGUCUUGAAA CACGGACCAA GGAGUCUAAC ACGUGCGCGA GUCGGG GGC UCGCACGAAA GCCGCCGUGG CGCAAUGAAG GUGAAGGCCG GCGCGCUCGC CGGCCGAGGU GGGAUCCCGA GGCCUCU CC AGUCCGCCGA GGGCGCACCA CCGGCCCGUC UCGCCCGCCG CGCCGGGGAG GUGGAGCACG AGCGCACGUG UUAGGACC C GAAAGAUGGU GAACUAUGCC UGGGCAGGGC GAAGCCAGAG GAAACUCUGG UGGAGGUCCG UAGCGGUCCU GACGUGCAA AUCGGUCGUC CGACCUGGGU AUAGGGGCGA AAGACUAAUC GAACCAUCUA GUAGCUGGUU CCCUCCGAAG UUUCCCUCAG GAUAGCUGG CGCUCUCGCA GACCCGACGC ACCCCCGCCA CGCAGUUUUA UCCGGUAAAG CGAAUGAUUA GAGGUCUUGG G GCCGAAAC GAUCUCAACC UAUUCUCAAA CUUUAAAUGG GUAAGAAGCC CGGCUCGCUG GCGUGGAGCC GGGCGUGGAA UG CGAGUGC CUAGUGGGCC ACUUUUGGUA AGCAGAACUG GCGCUGCGGG AUGAACCGAA CGCCGGGUUA AGGCGCCCGA UGC CGACGC UCAUCAGACC CCAGAAAAGG UGUUGGUUGA UAUAGACAGC AGGACGGUGG CCAUGGAAGU CGGAAUCCGC UAAG GAGUG UGUAACAACU CACCUGCCGA AUCAACUAGC CCUGAAAAUG GAUGGCGCUG GAGCGUCGGG CCCAUACCCG GCCGU CGCC GGCAGUCGAG AGUGGACGGG AGCGGCGGGG GCGGCGCGCG CGCGCGCGCG UGUGGUGUGC GUCGGAGGGC GGCGGC GGC GGCGGCGGCG GGGGUGUGGG GUCCUUCCCC CGCCCCCCCC CCCACGCCUC CUCCCCUCCU CCCGCCCACG CCCCGCU CC CCGCCCCCGG AGCCCCGCGG ACGCUACGCC GCGACGAGUA GGAGGGCCGC UGCGGUGAGC CUUGAAGCCU AGGGCGCG G GCCCGGGUGG AGCCGCCGCA GGUGCAGAUC UUGGUGGUAG UAGCAAAUAU UCAAACGAGA ACUUUGAAGG CCGAAGUGG AGAAGGGUUC CAUGUGAACA GCAGUUGAAC AUGGGUCAGU CGGUCCUGAG AGAUGGGCGA GCGCCGUUCC GAAGGGACGG GCGAUGGCC UCCGUUGCCC UCGGCCGAUC GAAAGGGAGU CGGGUUCAGA UCCCCGAAUC CGGAGUGGCG GAGAUGGGCG C CGCGAGGC GUCCAGUGCG GUAACGCGAC CGAUCCCGGA GAAGCCGGCG GGAGCCCCGG GGAGAGUUCU CUUUUCUUUG UG AAGGGCA GGGCGCCCUG GAAUGGGUUC GCCCCGAGAG AGGGGCCCGU GCCUUGGAAA GCGUCGCGGU UCCGGCGGCG UCC GGUGAG CUCUCGCUGG CCCUUGAAAA UCCGGGGGAG AGGGUGUAAA UCUCGCGCCG GGCCGUACCC AUAUCCGCAG CAGG UCUCC AAGGUGAACA GCCUCUGGCA UGUUGGAACA AUGUAGGUAA GGGAAGUCGG CAAGCCGGAU CCGUAACUUC GGGAU AAGG AUUGGCUCUA AGGGCUGGGU CGGUCGGGCU GGGGCGCGAA GCGGGGCUGG GCGCGCGCCG CGGCUGGACG AGGCGC CGC CGCCCCCCCC ACGCCCGGGG CACCCCCCUC GCGGCCCUCC CCCGCCCCAC CCCGCGCGCG CCGCUCGCUC CCUCCCC GC CCCGCGCCCU CUCUCUCUCU CUCUCCCCCG CUCCCCGUCC UCCCCCCUCC CCGGGGGAGC GCCGCGUGGG GGCGGCGG C GGGGGGAGAA GGGUCGGGGC GGCAGGGGCC GGCGGCGGCC CGCCGCGGGG CCCCGGCGGC GGGGGCACGG UCCCCCGCG AGGGGGGCCC GGGCACCCGG GGGGCCGGCG GCGGCGGCGA CUCUGGACGC GAGCCGGGCC CUUCCCGUGG AUCGCCCCAG CUGCGGCGG GCGUCGCGGC CGCCCCCGGG GAGCCCGGCG GGCGCCGGCG CGCCCCCCCC CCCACCCCAC GUCUCGUCGC G CGCGCGUC CGCUGGGGGC GGGGAGCGGU CGGGCGGCGG CGGUCGGCGG GCGGCGGGGC GGGGCGGUUC GUCCCCCCGC CC UACCCCC CCGGCCCCGU CCGCCCCCCG UUCCCCCCUC CUCCUCGGCG CGCGGCGGCG GCGGCGGCAG GCGGCGGAGG GGC CGCGGG CCGGUCCCCC CCGCCGGGUC CGCCCCCGGG GCCGCGGUUC CGCGCGGCGC CUCGCCUCGG CCGGCGCCUA GCAG CCGAC UUAGAACUGG UGCGGACCAG GGGAAUCCGA CUGUUUAAUU AAAACAAAGC AUCGCGAAGG CCCGCGGCGG GUGUU GACG CGAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAU GAAGCGCGGG UAAACGGCGG GAGUAA CUA UGACUCUCUU AAGGUAGCCA AAUGCCUCGU CAUCUAAUUA GUGACGCGCA UGAAUGGAUG AACGAGAUUC CCACUGU CC CUACCUACUA UCCAGCGAAA CCACAGCCAA GGGAACGGGC UUGGCGGAAU CAGCGGGGAA AGAAGACCCU GUUGAGCU U GACUCUAGUC UGGCACGGUG AAGAGACAUG AGAGGUGUAG AAUAAGUGGG AGGCCCCCGG CGCCCCCCCG GUGUCCCCG CGAGGGGCCC GGGGCGGGGU CCGCCGGCCC UGCGGGCCGC CGGUGAAAUA CCACUACUCU GAUCGUUUUU UCACUGACCC GGUGAGGCG GGGGGGCGAG CCCCGAGGGG CUCUCGCUUC UGGCGCCAAG CGCCCGGCCG CGCGCCGGCC GGGCGCGACC C GCUCCGGG GACAGUGCCA GGUGGGGAGU UUGACUGGGG CGGUACACCU GUCAAACGGU AACGCAGGUG UCCUAAGGCG AG CUCAGGG AGGACAGAAA CCUCCCGUGG AGCAGAAGGG CAAAAGCUCG CUUGAUCUUG AUUUUCAGUA CGAAUACAGA CCG UGAAAG CGGGGCCUCA CGAUCCUUCU GACCUUUUGG GUUUUAAGCA GGAGGUGUCA GAAAAGUUAC CACAGGGAUA ACUG GCUUG UGGCGGCCAA GCGUUCAUAG CGACGUCGCU UUUUGAUCCU UCGAUGUCGG CUCUUCCUAU CAUUGUGAAG CAGAA UUCA CCAAGCGUUG GAUUGUUCAC CCACUAAUAG GGAACGUGAG CUGGGUUUAG ACCGUCGUGA GACAGGUUAG UUUUAC CCU ACUGAUGAUG UGUUGUUGCC AUGGUAAUCC UGCUCAGUAC GAGAGGAACC GCAGGUUCAG ACAUUUGGUG UAUGUGC UU GGCUGAGGAG CCAAUGGGGC GAAGCUACCA UCUGUGGGAU UAUGACUGAA CGCCUCUAAG UCAGAAUCCC GCCCAGGC G GAACGAUACG GCAGCGCCGC GGAGCCUCGG UUGGCCUCGG AUAGCCGGUC CCCCGCCUGU CCCCGCCGGC GGGCCGCCC CCCCCCUCCA CGCGCCCCGC GCGCGCGGGA GGGCGCGUGC CCCGCCGCGC GCCGGGACCG GGGUCCGGUG CGGAGUGCCC UUCGUCCUG GGAAACGGGG CGCGGCCGGA GAGGCGGCCG CCCCCUCGCC CGUCACGCAC CGCACGUUCG UGGGGAACCU G GCGCUAAA CCAUUCGUAG ACGACCUGCU UCUGGGUCGG GGUUUCGUAC GUAGCAGAGC AGCUCCCUCG CUGCGAUCUA UU GAAAGUC AGCCCUCGAC ACAAGGGUUU GUC

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Macromolecule #2: Methionine aminopeptidase 1

MacromoleculeName: Methionine aminopeptidase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: methionyl aminopeptidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.717605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGSGSMAAV ETRVCETDGC SSEAKLQCPT CIKLGIQGSY FCSQECFKGS WATHKLLHKK AKDEKAKREV SSWTVEGDIN TDPWAGYRY TGKLRPHYPL MPTRPVPSYI QRPDYADHPL GMSESEQALK GTSQIKLLSS EDIEGMRLVC RLAREVLDVA A GMIKPGVT ...String:
GPGSGSMAAV ETRVCETDGC SSEAKLQCPT CIKLGIQGSY FCSQECFKGS WATHKLLHKK AKDEKAKREV SSWTVEGDIN TDPWAGYRY TGKLRPHYPL MPTRPVPSYI QRPDYADHPL GMSESEQALK GTSQIKLLSS EDIEGMRLVC RLAREVLDVA A GMIKPGVT TEEIDHAVHL ACIARNCYPS PLNYYNFPKS CCTSVNEVIC HGIPDRRPLQ EGDIVNVDIT LYRNGYHGDL NE TFFVGEV DDGARKLVQT TYECLMQAID AVKPGVRYRE LGNIIQKHAQ ANGFSVVRSY CGHGIHKLFH TAPNVPHYAK NKA VGVMKS GHVFTIEPMI CEGGWQDETW PDGWTAVTRD GKRSAQFEHT LLVTDTGCEI LTRRLDSARP HFMSQF

UniProtKB: Methionine aminopeptidase 1

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Macromolecule #3: Transcription factor BTF3

MacromoleculeName: Transcription factor BTF3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.201 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRRTGAPAQA DSRGRGRARG GCPGGEATLS QPPPRGGTRG QEPQMKETIM NQEKLAKLQA QVRIGGKGTA RRKKKVVHRT ATADDKKLQ FSLKKLGVNN ISGIEEVNMF TNQGTVIHFN NPKVQASLAA NTFTITGHAE TKQLTEMLPS ILNQLGADSL T SLRRLAEA ...String:
MRRTGAPAQA DSRGRGRARG GCPGGEATLS QPPPRGGTRG QEPQMKETIM NQEKLAKLQA QVRIGGKGTA RRKKKVVHRT ATADDKKLQ FSLKKLGVNN ISGIEEVNMF TNQGTVIHFN NPKVQASLAA NTFTITGHAE TKQLTEMLPS ILNQLGADSL T SLRRLAEA LPKQSVDGKA PLATGEDDDD EVPDLVENFD EASKNEAN

UniProtKB: Transcription factor BTF3

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Macromolecule #5: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.289338 KDa
SequenceString:
MKFNPFVTSD RSKNRKRHFN APSHIRRKIM SSPLSKELRQ KYNVRSMPIR KDDEVQVVRG HYKGQQIGKV VQVYRKKYVI YIERVQREK ANGTTVHVGI HPSKVVITRL KLDKDRKKIL ERKAKSRQVG KEKGKYKEET IEKMQD

UniProtKB: RPL26 protein

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Macromolecule #6: 60S ribosomal protein L35

MacromoleculeName: 60S ribosomal protein L35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.593624 KDa
SequenceString:
MAKIKARDLR GKKKEELLKQ LDDLKVELSQ LRVAKVTGGA ASKLSKIRVV RKSIARVLTV INQTQKENLR KFYKGKKYKP LDLRPKKTR AMRRRLNKHE ENLKTKKQQR KERLYPLRKY AVKA

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #7: 60S ribosomal protein L23a

MacromoleculeName: 60S ribosomal protein L23a / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.740193 KDa
SequenceString:
MAPKAKKEAP APPKAEAKAK ALKAKKAVLK GVHSHKKKKI RTSPTFRRPK TLRLRRQPKY PRKSAPRRNK LDHYAIIKFP LTTESAMKK IEDNNTLVFI VDVKANKHQI KQAVKKLYDI DVAKVNTLIR PDGEKKAYVR LAPDYDALDV ANKIGII

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #8: Nascent polypeptide-associated complex subunit alpha

MacromoleculeName: Nascent polypeptide-associated complex subunit alpha / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.849252 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSGSMPGE ATETVPATEQ ELPQPQAETG SGTESDSDES VPELEEQDST QATTQQAQLA AAAEIDEEPV SKAKQSRSEK KARKAMSKL GLRQVTGVTR VTIRKSKNIL FVITKPDVYK SPASDTYIVF GEAKIEDLSQ QAQLAAAEKF KVQGEAVSNI Q ENTQTPTV ...String:
GPGSGSMPGE ATETVPATEQ ELPQPQAETG SGTESDSDES VPELEEQDST QATTQQAQLA AAAEIDEEPV SKAKQSRSEK KARKAMSKL GLRQVTGVTR VTIRKSKNIL FVITKPDVYK SPASDTYIVF GEAKIEDLSQ QAQLAAAEKF KVQGEAVSNI Q ENTQTPTV QEESEEEEVD ETGVEVKDIE LVMSQANVSR AKAVRALKNN SNDIVNAIME LTM

UniProtKB: Nascent polypeptide-associated complex subunit alpha

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Macromolecule #9: 60S ribosomal protein L22

MacromoleculeName: 60S ribosomal protein L22 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.813015 KDa
SequenceString:
MAPVKKLVVK GGKKKKQVLK FTLDCTHPVE DGIMDAANFE QFLQERIKVN GKAGNLGGGV VTIERSKSKI TVTSEVPFSK RYLKYLTKK YLKKNNLRDW LRVVANSKES YELRYFQINQ DEEEEEDED

UniProtKB: Large ribosomal subunit protein eL22

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Macromolecule #10: 60S ribosomal protein L19

MacromoleculeName: 60S ribosomal protein L19 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.535281 KDa
SequenceString: MSMLRLQKRL ASSVLRCGKK KVWLDPNETN EIANANSRQQ IRKLIKDGLI IRKPVTVHSR ARCRKNTLAR RKGRHMGIGK RKGTANARM PEKVTWMRRM RILRRLLRRY RESKKIDRHM YHSLYLKVKG NVFKNKRILM EHIHKLKADK ARKKLLADQA E ARRSKTKE ...String:
MSMLRLQKRL ASSVLRCGKK KVWLDPNETN EIANANSRQQ IRKLIKDGLI IRKPVTVHSR ARCRKNTLAR RKGRHMGIGK RKGTANARM PEKVTWMRRM RILRRLLRRY RESKKIDRHM YHSLYLKVKG NVFKNKRILM EHIHKLKADK ARKKLLADQA E ARRSKTKE ARKRREERLQ AKKEEIIKTL SKEEETKK

UniProtKB: Large ribosomal subunit protein eL19

+
Macromolecule #11: 60S ribosomal protein L38

MacromoleculeName: 60S ribosomal protein L38 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.238948 KDa
SequenceString:
MPRKIEEIKD FLLTARRKDA KSVKIKKNKD NVKFKVRCSR YLYTLVITDK EKAEKLKQSL PPGLAVKELK

UniProtKB: Large ribosomal subunit protein eL38

+
Macromolecule #12: N-alpha-acetyltransferase 10

MacromoleculeName: N-alpha-acetyltransferase 10 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal amino-acid Nalpha-acetyltransferase NatA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.003795 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MGNIRNARPE DLMNMQHCNL LCLPENYQMK YYFYHGLSWP QLSYIAEDEN GKIVGYVLAK MEEDPDDVPH GHITSLAVKR SHRRLGLAQ KLMDQASRAM IENFNAKYVS LHVRKSNRAA LHLYSNTLNF QISEVEPKYY ADGEDAYAMK RDLTQMADEL R RHLELKEK GRH

UniProtKB: N-alpha-acetyltransferase 10

+
Macromolecule #13: N-alpha-acetyltransferase 15, NatA auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 15, NatA auxiliary subunit / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.658648 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPAVSLPPKE NALFKRILRC YEHKQYRNGL KFCKQILSNP KFAEHGETLA MKGLTLNCLG KKEEAYELVR RGLRNDLKSH VCWHVYGLL QRSDKKYDEA IKCYRNALKW DKDNLQILRD LSLLQIQMRD LEGYRETRYQ LLQLRPAQRA SWIGYAIAYH L LEDYEMAA ...String:
MPAVSLPPKE NALFKRILRC YEHKQYRNGL KFCKQILSNP KFAEHGETLA MKGLTLNCLG KKEEAYELVR RGLRNDLKSH VCWHVYGLL QRSDKKYDEA IKCYRNALKW DKDNLQILRD LSLLQIQMRD LEGYRETRYQ LLQLRPAQRA SWIGYAIAYH L LEDYEMAA KILEEFRKTQ QTSPDKVDYE YSELLLYQNQ VLREAGLYRE ALEHLCTYEK QICDKLAVEE TKGELLLQLC RL EDAADVY RGLQERNPEN WAYYKGLEKA LKPANMLERL KIYEEAWTKY PRGLVPRRLP LNFLSGEKFK ECLDKFLRMN FSK GCPPVF NTLRSLYKDK EKVAIIEELV VGYETSLKSC RLFNPNDDGK EEPPTTLLWV QYYLAQHYDK IGQPSIALEY INTA IESTP TLIELFLVKA KIYKHAGNIK EAARWMDEAQ ALDTADRFIN SKCAKYMLKA NLIKEAEEMC SKFTREGTSA VENLN EMQC MWFQTECAQA YKAMNKFGEA LKKCHEIERH FIEITDDQFD FHTYCMRKIT LRSYVDLLKL EDVLRQHPFY FKAARI AIE IYLKLHDNPL TDENKEHEAD TANMSDKELK KLRNKQRRAQ KKAQIEEEKK NAEKEKQQRN QKKKKDDDDE EIGGPKE EL IPEKLAKVET PLEEAIKFLT PLKNLVKNKI ETHLFAFEIY FRKEKFLLML QSVKRAFAID SSHPWLHECM IRLFNTVC E SKDLSDTVRT VLKQEMNRLF GATNPKNFNE TFLKRNSDSL PHRLSAAKMV YYLDPSSQKR AIELATTLDE SLTNRNLQT CMEVLEALYD GSLGDCKEAA EIYRANCHKL FPYALAFMPP

UniProtKB: N-alpha-acetyltransferase 15, NatA auxiliary subunit

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Macromolecule #14: 60S ribosomal protein L4

MacromoleculeName: 60S ribosomal protein L4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.804621 KDa
SequenceString: MACARPLISV YSEKGESSGK NVTLPAVFKA PIRPDIVNFV HTNLRKNNRQ PYAVSELAGH QTSAESWGTG RAVARIPRVR GGGTHRSGQ GAFGNMCRGG RMFAPTKTWR RWHRRVNTTQ KRYAICSALA ASALPALVMS KGHRIEEVPE LPLVVEDKVE G YKKTKEAV ...String:
MACARPLISV YSEKGESSGK NVTLPAVFKA PIRPDIVNFV HTNLRKNNRQ PYAVSELAGH QTSAESWGTG RAVARIPRVR GGGTHRSGQ GAFGNMCRGG RMFAPTKTWR RWHRRVNTTQ KRYAICSALA ASALPALVMS KGHRIEEVPE LPLVVEDKVE G YKKTKEAV LLLKKLKAWN DIKKVYASQR MRAGKGKMRN RRRIQRRGPC IIYNEDNGII KAFRNIPGIT LLNVSKLNIL KL APGGHVG RFCIWTESAF RKLDELYGTW RKAASLKSNY NLPMHKMINT DLSRILKSPE IQRALRAPRK KIHRRVLKKN PLK NLRIML KLNPYAKTMR RNTILRQARN HKLRVDKAAA AAAALQAKSD EKAAVAGKKP VVGKKGKKAA VGVKKQKKPL VGKK AAATK KPAPEKKPAE KKPTTEEKKP AA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #15: Large ribosomal subunit protein eL6

MacromoleculeName: Large ribosomal subunit protein eL6 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.810176 KDa
SequenceString: MAGEKVEKPD TKEKKPEAKK VDAGGKVKKG NLKAKKPKKG KPHCSRNPVL VRGIGRYSRS AMYSRKAMYK RKYSAAKSKV EKKKKEKVL ATVTKPVGGD KNGGTRVVKL RKMPRYYPTE DVPRKLLSHG KKPFSQHVRK LRASITPGTI LIILTGRHRG K RVVFLKQL ...String:
MAGEKVEKPD TKEKKPEAKK VDAGGKVKKG NLKAKKPKKG KPHCSRNPVL VRGIGRYSRS AMYSRKAMYK RKYSAAKSKV EKKKKEKVL ATVTKPVGGD KNGGTRVVKL RKMPRYYPTE DVPRKLLSHG KKPFSQHVRK LRASITPGTI LIILTGRHRG K RVVFLKQL ASGLLLVTGP LVLNRVPLRR THQKFVIATS TKIDISNVKI PKHLTDAYFK KKKLRKPRHQ EGEIFDTEKE KY EITEQRK IDQKAVDSQI LPKIKAIPQL QGYLRSVFAL TNGIYPHKLV F

UniProtKB: Large ribosomal subunit protein eL6

+
Macromolecule #16: 60S ribosomal protein L28

MacromoleculeName: 60S ribosomal protein L28 / type: protein_or_peptide / ID: 16
Details: SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGVEPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKN
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.784622 KDa
SequenceString:
MSAHLQWMVV RNCSSFLIKR NKQTYSTEPN NLKARNSFRY NGLIHRKTVG VEPAADGKGV VVVIKRRSGQ RKPATSYVRT TINKNARAT LSSIRHMIRK NKYRPDLRMA AIRRASAILR SQKPVMVKRK RTRPTKSS

UniProtKB: Large ribosomal subunit protein eL28

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Macromolecule #17: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 17 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 53.97 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24116
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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