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- EMDB-17002: Human Methionine Aminopeptidase 2 at the 80S ribosome -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-17002
TitleHuman Methionine Aminopeptidase 2 at the 80S ribosomeMethionyl aminopeptidase
Map data
Sample
  • Complex: MAP2-80S ribosome complex
    • RNA: 28S rRNA28S ribosomal RNA
    • Protein or peptide: 60S ribosomal protein L38
    • Protein or peptide: 60S ribosomal protein L26
    • Protein or peptide: 60S ribosomal protein L35
    • Protein or peptide: 60S ribosomal protein L23a
    • Protein or peptide: 60S ribosomal protein L19
    • RNA: 5.8S rRNA5.8S ribosomal RNA
    • Protein or peptide: Methionine aminopeptidase 2Methionyl aminopeptidase
  • Ligand: COBALT (II) ION
KeywordsRibosome Associated Factor / Protease / Tunnel exit / Protein Maturation / Proteostasis / NME / p67 / MAP / MetAP / MAP2 / MetAP2 / ES27L / PTE / METAL BINDING PROTEIN
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / eukaryotic 80S initiation complex / methionyl aminopeptidase / axial mesoderm development / 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 / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator ...N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / eukaryotic 80S initiation complex / methionyl aminopeptidase / axial mesoderm development / 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 / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / metalloexopeptidase activity / TORC2 complex binding / middle ear morphogenesis / Peptide chain elongation / Selenocysteine synthesis / metalloaminopeptidase activity / protein-RNA complex assembly / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / aminopeptidase activity / ribosomal large subunit biogenesis / ossification / cytosolic ribosome / positive regulation of translation / skeletal system development / sensory perception of sound / cellular response to gamma radiation / mRNA 5'-UTR binding / protein processing / rRNA processing / Regulation of expression of SLITs and ROBOs / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to UV / regulation of translation / cytoplasmic translation / cytosolic large ribosomal subunit / postsynaptic density / rRNA binding / structural constituent of ribosome / cadherin binding / ribonucleoprotein complex / translation / focal adhesion / mRNA binding / synapse / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase M24A, methionine aminopeptidase, subfamily 2 / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Ribosomal protein L23 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L38e / Ribosomal protein L38e superfamily ...Peptidase M24A, methionine aminopeptidase, subfamily 2 / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24, methionine aminopeptidase / Ribosomal protein L23 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L23, N-terminal domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L19 / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L24 signature. / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW / KOW motif / 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
Large ribosomal subunit protein uL29 / Methionine aminopeptidase 2 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL19
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsKlein MA / Wild K / Kisonaite M / Sinning I
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586-6 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome.
Authors: Marius A Klein / Klemens Wild / Miglė Kišonaitė / Irmgard Sinning /
Abstract: Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine ...Excision of the initiator methionine is among the first co-translational processes that occur at the ribosome. While this crucial step in protein maturation is executed by two types of methionine aminopeptidases in eukaryotes (MAP1 and MAP2), additional roles in disease and translational regulation have drawn more attention to MAP2. Here, we report several cryo-EM structures of human and fungal MAP2 at the 80S ribosome. Irrespective of nascent chains, MAP2 can occupy the tunnel exit. On nascent chain displaying ribosomes, the MAP2-80S interaction is highly dynamic and the MAP2-specific N-terminal extension engages in stabilizing interactions with the long rRNA expansion segment ES27L. Loss of this extension by autoproteolytic cleavage impedes interactions at the tunnel, while promoting MAP2 to enter the ribosomal A-site, where it engages with crucial functional centers of translation. These findings reveal that proteolytic remodeling of MAP2 severely affects ribosome binding, and set the stage for targeted functional studies.
History
DepositionApr 4, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17002.png

Downloads & links

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Map

FileDownload / File: emd_17002.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 720 pix.
= 799.2 Å		1.11 Å/pix.
x 720 pix.
= 799.2 Å		1.11 Å/pix.
x 720 pix.
= 799.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.82
Minimum - Maximum-3.4486167 - 7.3881807
Average (Standard dev.)-0.0043918504 (±0.15032806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 799.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17002_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Half map: #2

Fileemd_17002_half_map_2.map
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Sample components

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Entire : MAP2-80S ribosome complex

EntireName: MAP2-80S ribosome complex
Components
  • Complex: MAP2-80S ribosome complex
    • RNA: 28S rRNA28S ribosomal RNA
    • Protein or peptide: 60S ribosomal protein L38
    • Protein or peptide: 60S ribosomal protein L26
    • Protein or peptide: 60S ribosomal protein L35
    • Protein or peptide: 60S ribosomal protein L23a
    • Protein or peptide: 60S ribosomal protein L19
    • RNA: 5.8S rRNA5.8S ribosomal RNA
    • Protein or peptide: Methionine aminopeptidase 2Methionyl aminopeptidase
  • Ligand: COBALT (II) ION

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Supramolecule #1: MAP2-80S ribosome complex

SupramoleculeName: MAP2-80S ribosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 28S rRNA

MacromoleculeName: 28S rRNA / type: rna / ID: 1 / 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

GENBANK: GENBANK: NR_003287.4

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Macromolecule #7: 5.8S rRNA

MacromoleculeName: 5.8S rRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.449812 KDa
SequenceString:
CGACUCUUAG CGGUGGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGA CACAUUGAU CAUCGACACU UCGAACGCAC UUGCGGCCCC GGGUUCCUCC CGGGGCUACG CCUGUCUGAG CGUCGCUU

GENBANK: GENBANK: U13369.1

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Macromolecule #2: 60S ribosomal protein L38

MacromoleculeName: 60S ribosomal protein L38 / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: 60S ribosomal protein L26

MacromoleculeName: 60S ribosomal protein L26 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.303363 KDa
SequenceString:
MKFNPFVTSD RSKNRKRHFN APSHIRRKIM SSPLSKELRQ KYNVRSMPIR KDDEVQVVRG HYKGQQIGKV VQVYRKKYVI YIERVQREK ANGTTVHVGI HPSKVVITRL KLDKDRKKIL ERKAKSRQVG KEKGKYKEET IEKMQE

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #4: 60S ribosomal protein L35

MacromoleculeName: 60S ribosomal protein L35 / type: protein_or_peptide / ID: 4 / 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 #5: 60S ribosomal protein L23a

MacromoleculeName: 60S ribosomal protein L23a / type: protein_or_peptide / ID: 5 / 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 #6: 60S ribosomal protein L19

MacromoleculeName: 60S ribosomal protein L19 / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #8: Methionine aminopeptidase 2

MacromoleculeName: Methionine aminopeptidase 2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: methionyl aminopeptidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.971523 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MAGVEEVAAS GSHLNGDLDP DDREEGAAST AEEAAKKKRR KKKKSKGPSA AGEQEPDKES GASVDEVARQ LERSALEDKE RDEDDEDGD GDGDGATGKK KKKKKKKRGP KVQTDPPSVP ICDLYPNGVF PKGQECEYPP TQDGRTAAWR TTSEEKKALD Q ASEEIWND ...String:
MAGVEEVAAS GSHLNGDLDP DDREEGAAST AEEAAKKKRR KKKKSKGPSA AGEQEPDKES GASVDEVARQ LERSALEDKE RDEDDEDGD GDGDGATGKK KKKKKKKRGP KVQTDPPSVP ICDLYPNGVF PKGQECEYPP TQDGRTAAWR TTSEEKKALD Q ASEEIWND FREAAEAHRQ VRKYVMSWIK PGMTMIEICE KLEDCSRKLI KENGLNAGLA FPTGCSLNNC AAHYTPNAGD TT VLQYDDI CKIDFGTHIS GRIIDCAFTV TFNPKYDTLL KAVKDATNTG IKCAGIDVRL CDVGEAIQEV MESYEVEIDG KTY QVKPIR NLNGHSIGQY RIHAGKTVPI VKGGEATRME EGEVYAIETF GSTGKGVVHD DMECSHYMKN FDVGHVPIRL PRTK HLLNV INENFGTLAF CRRWLDRLGE SKYLMALKNL CDLGIVDPYP PLCDIKGSYT AQFEHTILLR PTCKEVVSRG DDY

UniProtKB: Methionine aminopeptidase 2

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Macromolecule #9: COBALT (II) ION

MacromoleculeName: COBALT (II) ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: CO
Molecular weightTheoretical: 58.933 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1b6a

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215768

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