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- PDB-9t6i: In vitro reconstituted METAP1-NAA40-NAC bound 80S - State 2 -

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Basic information

Entry
Database: PDB / ID: 9t6i
TitleIn vitro reconstituted METAP1-NAA40-NAC bound 80S - State 2
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal protein ...) x 37
  • (Large ribosomal subunit protein ...) x 6
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • Isoform 2 of Transcription factor BTF3
  • Methionine aminopeptidase 1
  • N-alpha-acetyltransferase 40
  • Nascent polypeptide-associated complex subunit alpha
  • Receptor of activated protein C kinase 1
  • Small ribosomal subunit protein eS4, X isoform
  • Ubiquitin
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
KeywordsRIBOSOME / 80S / co-translational / NAA40 / NAC / histone acetylation / N-terminal acetylation / human
Function / homology
Function and homology information


N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / protein N-terminal-serine acetyltransferase activity / regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue growth / positive regulation of cell proliferation involved in heart morphogenesis / cardiac ventricle development / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / heart trabecula morphogenesis ...N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / protein N-terminal-serine acetyltransferase activity / regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue growth / positive regulation of cell proliferation involved in heart morphogenesis / cardiac ventricle development / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / heart trabecula morphogenesis / histone H4 acetyltransferase activity / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / skeletal muscle tissue regeneration / embryonic brain development / translation at presynapse / response to insecticide / negative regulation of endoplasmic reticulum unfolded protein response / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / TNFR1-mediated ceramide production / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition / negative regulation of formation of translation preinitiation complex / nucleolus organization / positive regulation of ubiquitin-protein transferase activity / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA-templated transcription initiation / negative regulation of DNA repair / negative regulation of striated muscle cell apoptotic process / TORC2 complex binding / erythrocyte homeostasis / supercoiled DNA binding / regulation of establishment of cell polarity / rRNA modification in the nucleus and cytosol / oxidized purine DNA binding / NF-kappaB complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / cytoplasmic translational initiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of translation involved in cellular response to UV / metalloaminopeptidase activity / A band / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / laminin receptor activity / response to aldosterone / negative regulation of myoblast fusion / protein-DNA complex disassembly / Ribosomal scanning and start codon recognition / protein kinase A binding / Translation initiation complex formation / negative regulation of Wnt signaling pathway / positive regulation of DNA damage response, signal transduction by p53 class mediator / aminopeptidase activity / fibroblast growth factor binding / BH3 domain binding / Protein hydroxylation / TOR signaling / mTORC1-mediated signalling / negative regulation of translational frameshifting / monocyte chemotaxis / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SARS-CoV-1 modulates host translation machinery / regulation of cell division / positive regulation of GTPase activity / protein localization to nucleus / Peptide chain elongation / Selenocysteine synthesis / negative regulation of protein binding / Formation of a pool of free 40S subunits / negative regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein serine/threonine kinase inhibitor activity / protein targeting / Eukaryotic Translation Termination / Dengue Virus Attachment and Entry / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ubiquitin ligase inhibitor activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit
Similarity search - Function
N-alpha-acetyltransferase 40 / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / Nascent polypeptide-associated complex subunit alpha / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / NAC A/B domain superfamily ...N-alpha-acetyltransferase 40 / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / Nascent polypeptide-associated complex subunit alpha / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / : / Acetyltransferase (GNAT) family / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Gcn5-related N-acetyltransferase (GNAT) domain profile. / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / GNAT domain / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L13e / Ribosomal L38e protein family / Ribosomal protein S21e / Ribosomal protein L38e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / : / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L6e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Acyl-CoA N-acyltransferase / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Ribosomal protein L18/L18-A/B/e, conserved site / Plectin/S10 domain / Ribosomal protein L18e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein S30
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Transcription factor BTF3 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Methionine aminopeptidase 1 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Nascent polypeptide-associated complex subunit alpha / N-alpha-acetyltransferase 40 / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsGuan, D. / Berninghausen, O. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2026
Title: NAA40 and NAC cooperate in co-translational histone acetylation in humans.
Authors: Dandan Guan / Timo Denk / Ariel Klavaris / Matthias Thoms / Otto Berninghausen / Birgitta Beatrix / Antonis Kirmizis / Roland Beckmann /
Abstract: N-terminal acetylation is an abundant and predominantly co-translational modification in eukaryotes that profoundly affects folding, compartmentalization fidelity and turnover of target proteins. ...N-terminal acetylation is an abundant and predominantly co-translational modification in eukaryotes that profoundly affects folding, compartmentalization fidelity and turnover of target proteins. Unlike other N-acetyltransferases, human NatD is composed solely of the catalytic subunit NAA40 and exclusively modifies histone proteins H2A and H4. However, the molecular details of co-translational NAA40 activity have remained elusive. Here, we show biochemically and by cryo-EM how NAA40 activity is coordinated at the ribosomal peptide tunnel exit involving the NAC complex. We demonstrate that the NAA40-NAC interaction is required for efficient ribosome binding and histone acetylation. Furthermore, we provide insights on the potential coordination of methionine removal and subsequent NAA40-mediated acetylation by formation of a multienzyme complex on the ribosome involving METAP1. Therefore, our results illustrate the details of N-terminal histone acetylation by NAA40 and highlight the role of NAC as a general coordinator of nascent protein modification.
History
DepositionNov 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L5: 28S rRNA
L7: 5S rRNA
L8: 5.8S rRNA
LA: 60S ribosomal protein L8
LB: 60S ribosomal protein L3
LC: 60S ribosomal protein L4
LD: 60S ribosomal protein L5
LE: Large ribosomal subunit protein eL6
LF: Large ribosomal subunit protein uL30
LG: 60S ribosomal protein L7a
LH: 60S ribosomal protein L9
LI: 60S ribosomal protein L10
LJ: 60S ribosomal protein L11
LL: Large ribosomal subunit protein eL13
LM: 60S ribosomal protein L14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a
LP: 60S ribosomal protein L17
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LU: 60S ribosomal protein L22
LV: 60S ribosomal protein L23
LW: 60S ribosomal protein L24
LX: 60S ribosomal protein L23a
LY: 60S ribosomal protein L26
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L27a
Lb: 60S ribosomal protein L29
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Lh: 60S ribosomal protein L35
Li: 60S ribosomal protein L36
Lj: Large ribosomal subunit protein eL37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lm: Large ribosomal subunit protein eL40
Ln: 60S ribosomal protein L41
Lo: 60S ribosomal protein L36a
Lp: 60S ribosomal protein L37a
Lr: 60S ribosomal protein L28
Ls: 60S acidic ribosomal protein P0
Lt: Large ribosomal subunit protein uL11
MA: Methionine aminopeptidase 1
N4: N-alpha-acetyltransferase 40
NA: Nascent polypeptide-associated complex subunit alpha
NB: Isoform 2 of Transcription factor BTF3
S2: 18S rRNA
SA: 40S ribosomal protein SA
SB: 40S ribosomal protein S3a
SC: 40S ribosomal protein S2
SD: 40S ribosomal protein S3
SE: Small ribosomal subunit protein eS4, X isoform
SF: 40S ribosomal protein S5
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: 40S ribosomal protein S9
SK: 40S ribosomal protein S10
SL: 40S ribosomal protein S11
SM: 40S ribosomal protein S12
SN: 40S ribosomal protein S13
SO: 40S ribosomal protein S14
SP: 40S ribosomal protein S15
SQ: 40S ribosomal protein S16
SR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
SV: 40S ribosomal protein S21
SW: 40S ribosomal protein S15a
SX: 40S ribosomal protein S23
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sa: 40S ribosomal protein S26
Sb: 40S ribosomal protein S27
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Se: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Sf: Ubiquitin
Sg: Receptor of activated protein C kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,958,537350
Polymers3,951,76885
Non-polymers6,770265
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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RNA chain , 4 types, 4 molecules L5L7L8S2

#1: RNA chain 28S rRNA


Mass: 1640182.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 86475748
#2: RNA chain 5S rRNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#3: RNA chain 5.8S rRNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#52: RNA chain 18S rRNA


Mass: 602752.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36162

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60S ribosomal protein ... , 37 types, 37 molecules LALBLCLDLGLHLILJLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLgLh...

#4: Protein 60S ribosomal protein L8 / Large ribosomal subunit protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#5: Protein 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#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
#7: Protein 60S ribosomal protein L5 / Large ribosomal subunit protein uL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#10: Protein 60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#11: Protein 60S ribosomal protein L9 / Large ribosomal subunit protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#12: Protein 60S ribosomal protein L10 / Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein ...Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein L10 / Tumor suppressor QM


Mass: 24630.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635
#13: Protein 60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#15: Protein 60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#16: Protein 60S ribosomal protein L15 / Large ribosomal subunit protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#17: Protein 60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#18: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#19: Protein 60S ribosomal protein L18 / Large ribosomal subunit protein eL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#20: 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
#21: Protein 60S ribosomal protein L18a / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#22: Protein 60S ribosomal protein L21 / Large ribosomal subunit protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#23: 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
#24: Protein 60S ribosomal protein L23 / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#25: Protein 60S ribosomal protein L24 / 60S ribosomal protein L30 / Large ribosomal subunit protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#26: 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
#27: Protein 60S ribosomal protein L26 / Large ribosomal subunit protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#28: Protein 60S ribosomal protein L27 / Large ribosomal subunit protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#29: Protein 60S ribosomal protein L27a / Large ribosomal subunit protein uL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#30: Protein 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP / Large ribosomal subunit protein eL29


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#31: Protein 60S ribosomal protein L30 / Large ribosomal subunit protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#32: Protein 60S ribosomal protein L31 / Large ribosomal subunit protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#33: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#34: Protein 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#35: Protein 60S ribosomal protein L34 / Large ribosomal subunit protein eL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#36: 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
#37: Protein 60S ribosomal protein L36 / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#39: 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
#40: Protein 60S ribosomal protein L39 / Large ribosomal subunit protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#42: Protein/peptide 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#43: Protein 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / Large ribosomal subunit protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#44: Protein 60S ribosomal protein L37a / Large ribosomal subunit protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#45: 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 ... , 6 types, 6 molecules LELFLLLjLmLt

#8: 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 uL30 / 60S ribosomal protein L7


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#14: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#38: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#41: Protein Large ribosomal subunit protein eL40 / 60S ribosomal protein L40


Mass: 14771.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Naturally occurring methyl-lysine (MLZ) modification.
Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#47: Protein Large ribosomal subunit protein uL11 / 60S ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050

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Protein , 9 types, 9 molecules LsMAN4NANBSESeSfSg

#46: Protein 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E / Large ribosomal subunit protein uL10


Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388
#48: Protein Methionine aminopeptidase 1 / MAP 1 / MetAP 1 / Peptidase M 1


Mass: 43275.184 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
#49: Protein N-alpha-acetyltransferase 40 / N-acetyltransferase 11 / N-alpha-acetyltransferase D / NatD / hNatD / Protein acetyltransferase 1


Mass: 27236.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA40, NAT11, PATT1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86UY6, N-terminal L-serine Nalpha-acetyltransferase NatD
#50: Protein Nascent polypeptide-associated complex subunit alpha / NAC-alpha / Alpha-NAC


Mass: 23406.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NACA, HSD48 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13765
#51: Protein Isoform 2 of Transcription factor BTF3 / Nascent polypeptide-associated complex subunit beta / NAC-beta / RNA polymerase B transcription factor 3


Mass: 17724.037 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: Escherichia coli (E. coli) / References: UniProt: P20290
#57: Protein Small ribosomal subunit protein eS4, X isoform / 40S ribosomal protein S4 / SCR10 / Single copy abundant mRNA protein


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#83: Protein Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / FAU ubiquitin like and ribosomal protein S30 fusion


Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#84: Protein Ubiquitin


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#85: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244

+
40S ribosomal protein ... , 29 types, 29 molecules SASBSCSDSFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSd

#53: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#54: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#55: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#56: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#58: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#59: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#60: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#61: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#62: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#63: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#64: Protein 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#65: Protein 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 14548.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Sequence difference to the canonical Uniprot entry originates from CAA37582.1.
Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#66: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#67: Protein 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#68: Protein 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#69: Protein 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#70: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#71: Protein 40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#72: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#73: Protein 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#74: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#75: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#76: Protein 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#77: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#78: Protein 40S ribosomal protein S25 / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#79: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#80: Protein 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#81: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#82: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273

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Non-polymers , 2 types, 265 molecules

#86: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 257 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

-
Sample preparation

ComponentName: In vitro reconstituted METAP1-NAA40-NAC bound 80S - State 2
Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL
Molecular weightExperimental value: NO
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

-
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: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15772 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 103.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037237363
ELECTRON MICROSCOPYf_angle_d0.8107347734
ELECTRON MICROSCOPYf_chiral_restr0.041343157
ELECTRON MICROSCOPYf_plane_restr0.006723045
ELECTRON MICROSCOPYf_dihedral_angle_d14.672681898

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