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- PDB-9qqa: Ternary complex of translating ribosome, NAC and NMT1 -

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Basic information

Entry
Database: PDB / ID: 9qqa
TitleTernary complex of translating ribosome, NAC and NMT1
Components
  • (40S ribosomal protein ...) x 10
  • (60S ribosomal protein ...) x 21
  • (Large ribosomal subunit protein ...) x 9
  • (Ribosomal protein ...) x 10
  • (Small ribosomal subunit protein ...) x 20
  • (Ubiquitin-ribosomal protein ...) x 2
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • Glycylpeptide N-tetradecanoyltransferase 1
  • Isoform 2 of Transcription factor BTF3
  • Nascent chain
  • Nascent polypeptide-associated complex subunit alpha
  • P site Phe tRNA
  • S10_plectin domain-containing protein
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
  • [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
  • eL18
  • eS26
KeywordsRIBOSOME / Translation / co-translational protein processing
Function / homology
Function and homology information


negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / [histone H4]-lysine20 N-methyltransferase / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity ...negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / [histone H4]-lysine20 N-methyltransferase / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of skeletal muscle tissue growth / Late Phase of HIV Life Cycle / ketone metabolic process / histone H4K20 methyltransferase activity / regulation of opsin-mediated signaling pathway / cardiac ventricle development / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / heart trabecula morphogenesis / skeletal muscle tissue regeneration / ribosomal subunit / S-adenosyl-L-methionine binding / protein localization to membrane / laminin receptor activity / positive regulation of double-strand break repair via nonhomologous end joining / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 90S preribosome / 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 / phagocytic cup / pericentric heterochromatin / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / laminin binding / rough endoplasmic reticulum / eNOS activation / translation regulator activity / ribosomal small subunit export from nucleus / gastrulation / MDM2/MDM4 family protein binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / wound healing / Regulation of expression of SLITs and ROBOs / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / heparin binding / regulation of translation / protein transport / large ribosomal subunit / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium / methylation / perikaryon / killing of cells of another organism / cytosolic large ribosomal subunit / in utero embryonic development / cytoplasmic translation / cell differentiation / transcription coactivator activity / tRNA binding / negative regulation of translation / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome
Similarity search - Function
Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. ...Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / : / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / SET domain / Ribosomal protein L23 / SET domain profile. / SET domain superfamily / SET domain / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 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 L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L13e / S27a-like superfamily / Ribosomal protein L13e / 40S Ribosomal protein S10 / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Plectin/S10, N-terminal / Plectin/S10 domain
Similarity search - Domain/homology
SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 ...SPERMIDINE / SPERMINE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / 40S ribosomal protein S26 / Large ribosomal subunit protein eL28 / Ribosomal protein L32 / 60S ribosomal protein L36a-like / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Ribosomal protein L18 / 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 uL1 / 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 eL15 / Small ribosomal subunit protein uS11 / 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 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Ubiquitin-ribosomal protein eL40 fusion protein / Transcription factor BTF3 / Glycylpeptide N-tetradecanoyltransferase 1 / Large ribosomal subunit protein eL8 / Nascent polypeptide-associated complex subunit alpha / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsEcheverria, B. / Jaskolowski, M. / Scaiola, A. / Ban, N.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_212308 Switzerland
Swiss National Science Foundation51NF40-205601 Switzerland
European Research Council (ERC)101072047European Union
CitationJournal: Mol Cell / Year: 2025
Title: Mechanism of cotranslational protein N-myristoylation in human cells.
Authors: Martin Gamerdinger / Blanca Echeverria / Alfred M Lentzsch / Nicolas Burg / Ziyi Fan / Mateusz Jaskolowski / Alain Scaiola / Selina Piening / Shu-Ou Shan / Nenad Ban / Elke Deuerling /
Abstract: N-myristoyltransferases (NMTs) cotranslationally transfer the fatty acid myristic acid to the N terminus of newly synthesized proteins, regulating their function and cellular localization. These ...N-myristoyltransferases (NMTs) cotranslationally transfer the fatty acid myristic acid to the N terminus of newly synthesized proteins, regulating their function and cellular localization. These enzymes are important drug targets for the treatment of cancer and viral infections. N-myristoylation of nascent proteins occurs specifically on N-terminal glycine residues after the excision of the initiator methionine by methionine aminopeptidases (METAPs). How NMTs interact with ribosomes and gain timely and specific access to their substrates remains unknown. Here, we show that human NMT1 exchanges with METAP1 at the ribosomal tunnel exit to form an active cotranslational complex together with the nascent polypeptide-associated complex (NAC). NMT1 binding is sequence selective and specifically triggered by methionine excision, which exposes the N-myristoylation motif in the nascent chain. The revealed mode of interaction of NMT1 with NAC and the methionine-cleaved nascent protein elucidates how a specific subset of proteins can be efficiently N-myristoylated in human cells.
History
DepositionMar 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Jul 30, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A2: 18S rRNA
AA: Small ribosomal subunit protein eS27
AB: Small ribosomal subunit protein eS28
AC: Ubiquitin-ribosomal protein eS31 fusion protein
AD: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
AE: eS26
AF: Small ribosomal subunit protein RACK1
AG: Small ribosomal subunit protein uS14
AT: P site Phe tRNA
AZ: Small ribosomal subunit protein uS2
Aa: 40S ribosomal protein S3a
Ab: 40S ribosomal protein S2
Ac: 40S ribosomal protein S3
Ad: 40S ribosomal protein S4
Ae: Small ribosomal subunit protein uS7
Af: 40S ribosomal protein S6
Ag: 40S ribosomal protein S7
Ah: 40S ribosomal protein S8
Ai: Small ribosomal subunit protein uS4
Aj: S10_plectin domain-containing protein
Ak: Small ribosomal subunit protein uS17
Al: Small ribosomal subunit protein eS12
Am: Small ribosomal subunit protein uS15
An: Small ribosomal subunit protein uS11
Ao: Small ribosomal subunit protein uS19
Ap: Small ribosomal subunit protein uS9
Aq: Small ribosomal subunit protein eS17
Ar: Small ribosomal subunit protein uS13
As: 40S ribosomal protein S19
At: Small ribosomal subunit protein uS10
Au: Small ribosomal subunit protein eS21
Av: Small ribosomal subunit protein uS8
Aw: 40S ribosomal protein S23
Ax: 40S ribosomal protein S24
Ay: Small ribosomal subunit protein eS25
Az: Small ribosomal subunit protein eS32
B5: 28S rRNA
B7: 5S rRNA
B8: 5.8S rRNA
BA: Large ribosomal subunit protein uL2
BB: Ribosomal protein L3
BC: Large ribosomal subunit protein uL4
BE: 60S ribosomal protein L6
BF: Ribosomal Protein uL30
BG: 60S ribosomal protein L7a
BH: 60S ribosomal protein L9
BI: 60S ribosomal protein L10
BJ: 60S ribosomal protein L11
BK: Nascent chain
BL: Large ribosomal subunit protein eL13
BM: 60S ribosomal protein L14
BN: Ribosomal protein L15
BO: Large ribosomal subunit protein uL13
BP: Large ribosomal subunit protein uL22
BQ: eL18
BR: Ribosomal protein L19
BS: Large ribosomal subunit protein eL20
BT: 60S ribosomal protein L21
BU: 60S ribosomal protein L22
BV: Ribosomal protein L23
BW: Ribosomal protein L24
BX: Large ribosomal subunit protein uL23
BY: Ribosomal protein L26
BZ: 60S ribosomal protein L27
Ba: 60S ribosomal protein L27a
Bb: 60S ribosomal protein L29
Bc: 60S ribosomal protein L30
Bd: 60S ribosomal protein L31
Be: Ribosomal protein L32
Bf: 60S ribosomal protein L35a
Bg: 60S ribosomal protein L34
Bh: 60S ribosomal protein L35
Bi: 60S ribosomal protein L36
Bj: Ribosomal protein L37
Bk: 60S ribosomal protein L38
Bl: 60S ribosomal protein L39-like
Bm: Ubiquitin-ribosomal protein eL40 fusion protein
Bo: Large ribosomal subunit protein eL42
Bp: 60S ribosomal protein L37a
Br: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
Bs: Large ribosomal subunit protein uL10
Bt: 60S ribosomal protein L12
Bv: Ribosomal protein uL1
MA: Glycylpeptide N-tetradecanoyltransferase 1
Nt: Nascent polypeptide-associated complex subunit alpha
Nu: Isoform 2 of Transcription factor BTF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,954,487721
Polymers3,911,94686
Non-polymers42,541635
Water36,5342028
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 , 5 types, 5 molecules A2ATB5B7B8

#1: RNA chain 18S rRNA


Mass: 603928.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#9: RNA chain P site Phe tRNA


Mass: 24451.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 2082008580
#37: 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
#38: 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
#39: 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

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Small ribosomal subunit protein ... , 20 types, 20 molecules AAABAFAGAZAeAiAkAlAmAnAoApAqArAtAuAvAyAz

#2: Protein Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#3: Protein Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#7: 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
#8: Protein Small ribosomal subunit protein uS14 / uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#10: 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: 32822.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#15: Protein Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#19: Protein Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#21: Protein Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#22: Protein Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#23: Protein Small ribosomal subunit protein uS15 / uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#24: 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: G1T1F0
#25: Protein Small ribosomal subunit 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
#26: 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
#27: Protein Small ribosomal subunit 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
#28: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17654.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#30: Protein Small ribosomal subunit 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
#31: Protein Small ribosomal subunit protein eS21 / 40S ribosomal protein S21


Mass: 9165.375 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 uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#35: Protein Small ribosomal subunit protein eS25


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#36: Protein/peptide Small ribosomal subunit protein eS32


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

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Ubiquitin-ribosomal protein ... , 2 types, 2 molecules ACBm

#4: Protein Ubiquitin-ribosomal protein eS31 fusion protein


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#77: 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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Protein , 8 types, 8 molecules ADAEAjBQBrMANtNu

#5: Protein Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#6: Protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K5LQY6
#20: 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
#55: Protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: F6QKI9
#80: Protein [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B / [histone H4]-lysine20 N-methyltransferase KMT5B


Mass: 15697.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: A0A8C0DF35, [histone H4]-lysine20 N-methyltransferase, [histone H4]-N-methyl-L-lysine20 N-methyltransferase
#84: Protein Glycylpeptide N-tetradecanoyltransferase 1 / Myristoyl-CoA:protein N-myristoyltransferase 1 / HsNMT1 / NMT 1 / Type I N-myristoyltransferase / ...Myristoyl-CoA:protein N-myristoyltransferase 1 / HsNMT1 / NMT 1 / Type I N-myristoyltransferase / Peptide N-myristoyltransferase 1 / Protein-lysine myristoyltransferase NMT1


Mass: 56791.930 Da / Num. of mol.: 1 / Mutation: Y180A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: Escherichia coli (E. coli)
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#85: 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
#86: 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

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40S ribosomal protein ... , 10 types, 10 molecules AaAbAcAdAfAgAhAsAwAx

#11: 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
#12: Protein 40S ribosomal protein S2


Mass: 31285.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: O18789
#13: 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
#14: 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
#16: 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
#17: 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
#18: 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
#29: 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
#33: 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
#34: 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

+
Large ribosomal subunit protein ... , 9 types, 9 molecules BABCBLBOBPBSBXBoBs

#40: 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
#42: Protein Large ribosomal subunit protein uL4 / 60S ribosomal protein L4


Mass: 46283.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#50: 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
#53: 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
#54: 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
#57: 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
#62: 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
#78: 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
#81: 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

+
Ribosomal protein ... , 10 types, 10 molecules BBBFBNBRBVBWBYBeBjBv

#41: 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
#44: 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
#52: 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
#56: 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
#60: 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
#61: 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
#63: 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
#69: 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
#74: 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
#83: Protein Ribosomal protein uL1


Mass: 24875.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

+
60S ribosomal protein ... , 21 types, 21 molecules BEBGBHBIBJBMBTBUBZBaBbBcBdBfBgBhBiBkBlBpBt

#43: 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
#45: 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) Oryctolagus cuniculus (rabbit) / References: UniProt: P62424
#46: 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
#47: 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
#48: 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
#51: 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
#58: 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
#59: 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
#64: 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
#65: 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
#66: 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
#67: 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
#68: 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
#70: 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
#71: 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
#72: 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
#73: 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
#75: 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
#79: 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
#82: 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

+
Protein/peptide , 1 types, 1 molecules BK

#49: Protein/peptide Nascent chain


Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

+
Non-polymers , 6 types, 2663 molecules

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


Mass: 24.305 Da / Num. of mol.: 407 / Source method: obtained synthetically / Formula: Mg
#88: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 145.246 Da / Num. of mol.: 187 / Source method: obtained synthetically
#89: 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
#90: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#91: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn
#92: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2028 / Source method: isolated from a natural source / Formula: H2O

+
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ternary complex of translating ribosome, NAC and NMT1 / Type: RIBOSOME / Entity ID: #1-#86 / Source: NATURAL
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE

-
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: 2700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87143 / Symmetry type: POINT
RefinementCross valid method: NONE

+
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