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- PDB-9f1d: Mammalian quaternary complex of a translating 80S ribosome, NAC, ... -

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Basic information

Entry
Database: PDB / ID: 9f1d
TitleMammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK
Components
  • (40S ribosomal protein ...) x 21
  • (60S ribosomal protein ...) x 21
  • (Isoform 2 of ...) x 2
  • (Large ribosomal subunit protein ...) x 13
  • (N-alpha-acetyltransferase ...) x 2
  • (Ribosomal protein ...) x 12
  • (Small ribosomal subunit protein ...) x 8
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • Glutathione S-transferase class-mu 26 kDa isozyme,N-alpha-acetyltransferase 50,N-alpha-acetyltransferase 50
  • Methionine aminopeptidase 1
  • Nascent chain
  • Nascent polypeptide-associated complex subunit alpha
  • P-site tRNA
  • S10_plectin domain-containing protein
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • mRNA
KeywordsTRANSLATION / ribosome / NAC / N-terminal acetyltransferase / NatA / NatE / MetAP1 / HYPK
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / positive regulation of protein refolding / N-terminal methionine Nalpha-acetyltransferase NatE / mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / negative regulation of striated muscle cell apoptotic process / NatA complex / protein N-terminal-methionine acetyltransferase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / positive regulation of protein refolding / N-terminal methionine Nalpha-acetyltransferase NatE / mitotic sister chromatid cohesion, centromeric / protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal protein amino acid acetylation / negative regulation of striated muscle cell apoptotic process / NatA complex / protein N-terminal-methionine acetyltransferase activity / regulation of skeletal muscle fiber development / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / protein-N-terminal amino-acid acetyltransferase activity / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cardiac ventricle development / heart trabecula morphogenesis / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / histone H4 acetyltransferase activity / N-acetyltransferase activity / acetyltransferase activator activity / skeletal muscle tissue regeneration / establishment of mitotic sister chromatid cohesion / metalloexopeptidase activity / mitotic sister chromatid cohesion / metalloaminopeptidase activity / laminin receptor activity / Dengue Virus Genome Translation and Replication / aminopeptidase activity / protein-lysine-acetyltransferase activity / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein-RNA complex assembly / gastrulation / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / laminin binding / protein folding chaperone / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / MDM2/MDM4 family protein binding / post-translational protein modification / positive regulation of apoptotic signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / wound healing / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein maturation / small-subunit processome / platelet aggregation / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / regulation of translation / microtubule cytoskeleton / rhythmic process / heparin binding / antimicrobial humoral immune response mediated by antimicrobial peptide / protein transport / Inactivation, recovery and regulation of the phototransduction cascade / large ribosomal subunit / ribosomal small subunit assembly / virus receptor activity / ribosome binding / angiogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / transcription regulator complex / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / killing of cells of another organism / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / perikaryon / nuclear body / cell differentiation / cytoplasmic translation / transcription coactivator activity / tRNA binding / mitochondrial inner membrane / postsynaptic density / negative regulation of translation / protein stabilization / rRNA binding / structural constituent of ribosome / ribosome / translation
Similarity search - Function
Huntingtin-interacting protein K, UBA-like domain / : / : / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Nascent polypeptide-associated complex subunit alpha / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. ...Huntingtin-interacting protein K, UBA-like domain / : / : / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Nascent polypeptide-associated complex subunit alpha / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / 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 / Tetratricopeptide repeat / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ubiquitin-like protein FUBI / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L30e / Gcn5-related N-acetyltransferase (GNAT) domain profile. / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / GNAT domain / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / TPR repeat region circular profile. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / : / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L6e signature. / TPR repeat profile. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Plectin/S10 domain / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Acyl-CoA N-acyltransferase / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Ribosomal protein L32 / 60S ribosomal protein L36a-like / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL15 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Ribosomal protein L19 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Ubiquitin-ribosomal protein eL40 fusion protein / Transcription factor BTF3 / N-alpha-acetyltransferase 10 / Methionine aminopeptidase 1 / Nascent polypeptide-associated complex subunit alpha / N-alpha-acetyltransferase 15, NatA auxiliary subunit / N-alpha-acetyltransferase 50 / Huntingtin-interacting protein K / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Schistosoma japonicum (invertebrata)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsYudin, D. / Scaiola, A. / Ban, N.
Funding support United States, Germany, Switzerland, European Union, 5items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR35 GM136321 United States
German Research Foundation (DFG)SFB969/A01 and A07 Germany
Swiss National Science Foundation310030_212308 Switzerland
Swiss National Science Foundation51NF40-205601 Switzerland
European Research Council (ERC)Synergy Grant 101072047European Union
CitationJournal: Nature / Year: 2024
Title: NAC guides a ribosomal multienzyme complex for nascent protein processing.
Authors: Alfred M Lentzsch / Denis Yudin / Martin Gamerdinger / Sowmya Chandrasekar / Laurenz Rabl / Alain Scaiola / Elke Deuerling / Nenad Ban / Shu-Ou Shan /
Abstract: Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), ...Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively. Both modifications are strictly cotranslational and essential in higher eukaryotic organisms. The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells.
History
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B5: 28S rRNA
BT: 60S ribosomal protein L21
Bb: 60S ribosomal protein L29
Bt: 60S ribosomal protein L12
AH: mRNA
Aq: 40S ribosomal protein eS17
B7: 5S rRNA
AT: P-site tRNA
Ar: Small ribosomal subunit protein uS13
B8: 5.8S rRNA
BU: 60S ribosomal protein L22
As: 40S ribosomal protein S19
BA: Large ribosomal subunit protein uL2
BV: Ribosomal protein L23
At: 40S ribosomal protein uS10
BB: Ribosomal protein L3
BP: Large ribosomal subunit protein uL22
BY: Ribosomal protein L26
Av: Ribosomal protein S15a
B: Large ribosomal subunit protein uL18
BX: Large ribosomal subunit protein uL23
BQ: Large ribosomal subunit protein eL18
BZ: 60S ribosomal protein L27
Aw: 40S ribosomal protein S23
BE: 60S ribosomal protein L6
BW: Ribosomal protein L24
Au: Small ribosomal subunit protein eS21
Ba: 60S ribosomal protein L27a
Ax: 40S ribosomal protein S24
BF: Ribosomal Protein uL30
BR: Ribosomal protein L19
AZ: Small ribosomal subunit protein uS2
Ay: 40S ribosomal protein S25
BG: Large ribosomal subunit protein eL8
BC: Large ribosomal subunit protein uL4
BS: Large ribosomal subunit protein eL20
Aa: 40S ribosomal protein S3a
Az: 60S ribosomal protein L41
BH: 60S ribosomal protein L9
EA: Methionine aminopeptidase 1
Ab: Small ribosomal subunit protein uS5
Bc: 60S ribosomal protein L30
BI: 60S ribosomal protein L10
Ct: Nascent polypeptide-associated complex subunit alpha
Ac: 40S ribosomal protein S3
Bd: 60S ribosomal protein L31
BJ: 60S ribosomal protein L11
Cu: Isoform 2 of Transcription factor BTF3
Ad: 40S ribosomal protein S4
Be: Ribosomal protein L32
BK: Nascent chain
DA: Glutathione S-transferase class-mu 26 kDa isozyme,N-alpha-acetyltransferase 50,N-alpha-acetyltransferase 50
Ae: Ribosomal protein S5
Bf: 60S ribosomal protein L35a
BL: Large ribosomal subunit protein eL13
DB: N-alpha-acetyltransferase 15, NatA auxiliary subunit
Af: 40S ribosomal protein S6
Bg: 60S ribosomal protein L34
BM: 60S ribosomal protein L14
DC: N-alpha-acetyltransferase 10
Ag: 40S ribosomal protein S7
Bh: 60S ribosomal protein L35
BN: Ribosomal protein L15
DD: Isoform 2 of Huntingtin-interacting protein K
Ah: 40S ribosomal protein S8
Bi: 60S ribosomal protein L36
BO: Large ribosomal subunit protein uL13
A2: 18S rRNA
Ai: 40S ribosomal protein S9
Bj: Ribosomal protein L37
AA: 40S ribosomal protein S27
Aj: S10_plectin domain-containing protein
Bk: 60S ribosomal protein L38
AB: 40S ribosomal protein S28
Ak: 40S ribosomal protein S11
Bl: 60S ribosomal protein L39-like
AC: Ribosomal protein S27a
Al: 40S ribosomal protein S12
Bm: Ubiquitin-ribosomal protein eL40 fusion protein
AD: 40S ribosomal protein S30
Am: 40S ribosomal protein S13
Bo: Large ribosomal subunit protein eL42
AE: Small ribosomal subunit protein eS26
An: Small ribosomal subunit protein uS11
Bp: 60S ribosomal protein L37a
AF: Small ribosomal subunit protein RACK1
Ao: 40S ribosomal protein uS19
Br: Large ribosomal subunit protein eL28
AG: 40S ribosomal protein S29
Ap: Small ribosomal subunit protein uS9
Bs: Large ribosomal subunit protein uL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,125,657849
Polymers4,108,77891
Non-polymers16,879758
Water38,1382117
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 , 6 types, 6 molecules B5AHB7ATB8A2

#1: RNA chain 28S rRNA


Mass: 1557519.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCN01009604.1
#5: RNA chain mRNA


Mass: 543.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: RNA chain 5S rRNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 4CXE_4
#8: RNA chain P-site tRNA


Mass: 15209.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#10: RNA chain 5.8S rRNA


Mass: 50809.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCN01009604.1
#68: RNA chain 18S rRNA


Mass: 603928.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: GBCT01000564.1

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60S ribosomal protein ... , 21 types, 21 molecules BTBbBtBUBZBEBaAzBHBcBIBdBJBfBgBMBhBiBkBlBp

#2: Protein 60S ribosomal protein L21 / eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#3: Protein 60S ribosomal protein L29


Mass: 26721.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#4: Protein 60S ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#11: Protein 60S ribosomal protein L22


Mass: 14756.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TSG1
#23: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#25: Protein 60S ribosomal protein L6


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#28: Protein 60S ribosomal protein L27a


Mass: 16635.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#38: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4
#39: Protein 60S ribosomal protein L9


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#42: Protein 60S ribosomal protein L30 / eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#43: Protein 60S ribosomal protein L10 / Ribosomal protein L10


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#46: Protein 60S ribosomal protein L31 / eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#47: Protein 60S ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#54: Protein 60S ribosomal protein L35a / eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#58: Protein 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#59: Protein 60S ribosomal protein L14


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#62: Protein 60S ribosomal protein L35 / uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#66: Protein 60S ribosomal protein L36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#73: Protein 60S ribosomal protein L38 / eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U001
#76: Protein 60S ribosomal protein L39-like / eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#85: Protein 60S ribosomal protein L37a / eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53

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40S ribosomal protein ... , 21 types, 21 molecules AqAsAtAwAxAyAaAcAdAfAgAhAiAAABAkAlADAmAoAG

#6: Protein 40S ribosomal protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#12: Protein 40S ribosomal protein S19


Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#15: Protein 40S ribosomal protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#24: Protein 40S ribosomal protein S23


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#29: Protein 40S ribosomal protein S24


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8
#33: Protein 40S ribosomal protein S25


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#37: Protein 40S ribosomal protein S3a / RPS3A


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#45: Protein 40S ribosomal protein S3 / uS3


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#49: Protein 40S ribosomal protein S4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#57: Protein 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#61: Protein 40S ribosomal protein S7


Mass: 47356.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#65: Protein 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#69: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#71: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#74: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#75: Protein 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#78: Protein 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#80: Protein 40S ribosomal protein S30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#81: Protein 40S ribosomal protein S13 / uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#87: Protein 40S ribosomal protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#89: Protein 40S ribosomal protein S29 / uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4

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Small ribosomal subunit protein ... , 8 types, 8 molecules ArAuAZAbAEAnAFAp

#9: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17670.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#27: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9181.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#32: Protein Small ribosomal subunit protein uS2 / 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 / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32838.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#41: Protein Small ribosomal subunit protein uS5


Mass: 31285.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: Protein Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#84: Protein Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0AAA9WYR1
#86: Protein Small ribosomal subunit protein RACK1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#90: Protein Small ribosomal subunit protein uS9 / uS9


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4

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Large ribosomal subunit protein ... , 13 types, 13 molecules BABPBBXBQBGBCBSBLBOBoBrBs

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


Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#17: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#20: Protein Large ribosomal subunit protein uL18 / uL18


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZF4
#21: Protein Large ribosomal subunit protein uL23 / uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#22: Protein Large ribosomal subunit protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: Protein Large ribosomal subunit protein eL8


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#35: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 46299.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#36: Protein Large ribosomal subunit protein eL20 / 60S ribosomal protein L18a


Mass: 20749.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTY7
#55: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#67: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVS8
#82: Protein Large ribosomal subunit protein eL42


Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0AAA9WX15
#88: Protein Large ribosomal subunit protein eL28 / 60S ribosomal protein L28


Mass: 15713.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#91: Protein Large ribosomal subunit protein uL10 / uL10


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4

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Ribosomal protein ... , 12 types, 12 molecules BVBBBYAvBWBFBRBeAeBNBjAC

#14: Protein Ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#16: Protein Ribosomal protein L3


Mass: 46120.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#18: Protein Ribosomal protein L26


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#19: Protein Ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#26: Protein Ribosomal protein L24 / eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#30: Protein Ribosomal Protein uL30


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1
#31: Protein Ribosomal protein L19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJR3
#50: Protein Ribosomal protein L32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0AAA9WVN6
#53: Protein Ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#63: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#70: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#77: Protein Ribosomal protein S27a


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22

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Protein , 5 types, 5 molecules EACtDAAjBm

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


Mass: 43274.195 Da / Num. of mol.: 1 / Mutation: D220N
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
#44: Protein Nascent polypeptide-associated complex subunit alpha / NAC-alpha / Alpha-NAC


Mass: 25857.480 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
#52: Protein Glutathione S-transferase class-mu 26 kDa isozyme,N-alpha-acetyltransferase 50,N-alpha-acetyltransferase 50 / hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog ...hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN / N-epsilon-acetyltransferase 50 / NatE catalytic subunit


Mass: 46529.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Homo sapiens (human)
Gene: NAA50, MAK3, NAT13, NAT5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9GZZ1, glutathione transferase, N-terminal methionine Nalpha-acetyltransferase NatE, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#72: Protein S10_plectin domain-containing protein / eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#79: Protein Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14800.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P0DXC2

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Isoform 2 of ... , 2 types, 2 molecules CuDD

#48: 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
#64: Protein Isoform 2 of Huntingtin-interacting protein K / Huntingtin yeast partner K


Mass: 26119.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HYPK, C15orf63, HSPC136 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NX55

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Protein/peptide , 1 types, 1 molecules BK

#51: Protein/peptide Nascent chain


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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

#56: Protein N-alpha-acetyltransferase 15, NatA auxiliary subunit / Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / ...Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / Protein tubedown-1 / Tbdn100


Mass: 106506.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA15, GA19, NARG1, NATH, TBDN100 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9BXJ9
#60: Protein N-alpha-acetyltransferase 10 / N-terminal acetyltransferase complex ARD1 subunit homolog A / hARD1 / NatA catalytic subunit Naa10


Mass: 26479.580 Da / Num. of mol.: 1 / Mutation: E24Q, Y26F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA10, ARD1, ARD1A, TE2 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA

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Non-polymers , 8 types, 2875 molecules

#92: Chemical...
ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 295 / Source method: obtained synthetically
#93: Chemical...
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C7H19N3
#94: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 420 / Source method: obtained synthetically / Formula: Mg
#95: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#96: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#97: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#98: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#99: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2117 / Source method: isolated from a natural source / Formula: H2O

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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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPKRIBOSOME#1, #17, #22, #26, #31, #36, #40, #44, #48, #52, #56, #60, #64, #68, #71, #74, #77, #80, #83, #86, #89, #2, #5, #8, #11, #14, #21, #18, #23, #28, #32, #37, #41, #45, #49, #53, #57, #61, #65, #69, #72, #75, #78, #81, #87, #90, #3, #6, #9, #12, #15, #27, #19, #24, #29, #33, #38, #42, #46, #50, #54, #58, #62, #66, #70, #73, #76, #79, #82, #85, #88, #91, #4, #7, #10, #13, #16, #35, #25, #30, #34, #39, #43, #47, #51, #55, #59, #63, #670MULTIPLE SOURCES
2Rabbit ribosome-nascent chain complexCOMPLEX#1, #17, #22, #26, #31, #36, #68, #71, #74, #77, #80, #83, #86, #89, #2, #5, #8, #11, #14, #21, #18, #23, #28, #32, #37, #41, #45, #49, #53, #57, #61, #65, #69, #72, #75, #78, #81, #87, #90, #3, #6, #9, #12, #15, #27, #19, #24, #29, #33, #38, #42, #46, #50, #54, #58, #62, #66, #70, #73, #76, #79, #82, #85, #88, #91, #4, #7, #10, #13, #16, #35, #25, #30, #34, #39, #43, #47, #51, #55, #59, #63, #671NATURAL
3Human NAC heterodimerCOMPLEX#44, #481RECOMBINANT
4Human methionine aminopeptidase 1COMPLEX#401RECOMBINANT
5Human NatA/E-HYPK complexCOMPLEX#52, #56, #60, #641MULTIPLE SOURCES
6Human NatA complexCOMPLEX#56, #604RECOMBINANT
7Human HYPKCOMPLEX#644RECOMBINANT
8Human NatE with a GST tagCOMPLEX#524RECOMBINANT
Molecular weightValue: 3.50 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Oryctolagus cuniculus (rabbit)9986
33Homo sapiens (human)9606
44Homo sapiens (human)9606
66Homo sapiens (human)9606
77Homo sapiens (human)9606
88Homo sapiens (human)9606
98Schistosoma japonicum (invertebrata)6182
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
33Escherichia coli (E. coli)562
44Escherichia coli (E. coli)562
66Saccharomyces cerevisiae (brewer's yeast)4932
77Escherichia coli (E. coli)562
88Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23034 / Symmetry type: POINT

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

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Aug 12, 2020. Covid-19 info

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