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Yorodumi- PDB-9syr: Human quaternary complex of a translating 80S ribosome, NAC, MetA... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9syr | ||||||||||||||||||||||||||||||||||||
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| Title | Human quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatD | ||||||||||||||||||||||||||||||||||||
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Keywords | RIBOSOME / translation / NAC / N-terminal acetyltransferase / NatD / MetAP1 | ||||||||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationN-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / protein N-terminal-serine acetyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cardiac ventricle development ...N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / protein N-terminal-serine acetyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / positive regulation of skeletal muscle tissue growth / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / cardiac ventricle development / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / histone H4 acetyltransferase activity / SUMOylation of DNA replication proteins / heart trabecula morphogenesis / metalloexopeptidase activity / skeletal muscle tissue regeneration / embryonic brain development / SUMOylation of SUMOylation proteins / translation at presynapse / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / exit from mitosis / optic nerve development / regulation of translation involved in cellular response to UV / SUMOylation of RNA binding proteins / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of ubiquitin-protein transferase activity / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / SUMOylation of chromatin organization proteins / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / positive regulation of DNA-templated transcription initiation / alpha-beta T cell differentiation / TNFR1-mediated ceramide production / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / negative regulation of RNA splicing / TORC2 complex binding / neural crest cell differentiation / supercoiled DNA binding / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / cytoplasmic translational initiation / muscle organ development / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / rRNA modification in the nucleus and cytosol / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / metalloaminopeptidase activity / ion channel inhibitor activity / laminin receptor activity / protein kinase A binding / homeostatic process / pigmentation / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / macrophage chemotaxis / lung morphogenesis / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / fibroblast growth factor binding / monocyte chemotaxis / BH3 domain binding / Protein hydroxylation Similarity search - Function | ||||||||||||||||||||||||||||||||||||
| Biological species | Homo sapiens (human)![]() ![]() Brachypodium distachyon (stiff brome) | ||||||||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å | ||||||||||||||||||||||||||||||||||||
Authors | Yudin, D. / Jaskolowski, M. / Scaiola, A. / Ban, N. | ||||||||||||||||||||||||||||||||||||
| Funding support | European Union, Switzerland, Germany, United States, 5items
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Citation | Journal: Sci Adv / Year: 2025Title: Mechanism of cotranslational modification of histones H2A and H4 by MetAP1 and NatD. Authors: Denis Yudin / Mateusz Jaskolowski / Ziyi Fan / Nicolas Burg / Sowmya Chandrasekar / Alfred M Lentzsch / Alain Scaiola / Adrian Bothe / Elke Deuerling / Martin Gamerdinger / Shu-Ou Shan / Nenad Ban / ![]() Abstract: The replication-dependent histones H2A and H4 are among the most highly expressed proteins in eukaryotes during the S phase to ensure packaging of replicated chromosomes. Nearly all newly synthesized ...The replication-dependent histones H2A and H4 are among the most highly expressed proteins in eukaryotes during the S phase to ensure packaging of replicated chromosomes. Nearly all newly synthesized H2A and H4 are N-terminally acetylated by N-terminal acetyltransferase D (NatD) following excision of the initiator methionine by methionine aminopeptidases (MetAPs). These modifications influence chromatin function, but how they occur cotranslationally on these exceptionally abundant and small proteins was not understood. Here, we show that the nascent polypeptide-associated complex controls the cotranslational modification of histones H2A and H4 by recruiting NatD and the upstream enzyme MetAP1 to ribosomes. MetAP1 and NatD cooperate on the ribosome to create a confined environment for the efficient sequential modification of the nascent histone chain. Our work provides a mechanistic model for the early steps of histone maturation. | ||||||||||||||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9syr.cif.gz | 4.9 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9syr.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9syr.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/9syr ftp://data.pdbj.org/pub/pdb/validation_reports/sy/9syr | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 55351MC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-RNA chain , 6 types, 6 molecules L1S1S2S3L2L3
| #1: RNA chain | Mass: 1641159.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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| #30: RNA chain | Mass: 603609.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
| #31: RNA chain | Mass: 588968.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
| #32: RNA chain | Mass: 24452.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
| #48: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898 |
| #68: RNA chain | Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853 |
+60S ribosomal protein ... , 36 types, 36 molecules LcLdLgLhLiLjLkLlLmLnLoLpLqLrLsLtLuLvLwLxLyLzSqLBLCLELFLGLHLJ...
-Large ribosomal subunit protein ... , 5 types, 5 molecules LeLfLALILP
| #4: Protein | Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878 |
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| #5: Protein | Mass: 23202.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429 |
| #69: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927 |
| #77: Protein | Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124 |
| #83: Protein | Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373 |
-Protein , 8 types, 8 molecules NaNbNmShSrSsLDLN
| #26: Protein | 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: ![]() |
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| #27: Protein | 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: ![]() |
| #29: Protein | Mass: 43274.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1, KIAA0094 / Production host: ![]() |
| #49: Protein | Mass: 15237.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847 |
| #59: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979 |
| #60: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244 |
| #72: Protein | Mass: 11470.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
| #81: Protein | Mass: 45314.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Brachypodium distachyon (stiff brome), (gene. exp.) Homo sapiens (human)Gene: GFP, SUMO1, SMT3, SUM1, Os01g0918300, LOC_Os01g68950, OsJ_04555, P0413C03.34-1, P0678F11.1-1, XBP1 Production host: Homo sapiens (human)References: UniProt: P42212, UniProt: P55857, UniProt: B1AHH2 |
-Ubiquitin-like ... , 2 types, 2 molecules NdSn
| #28: Protein | Mass: 41585.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Homo sapiens (human)Gene: SMT3, YDR510W, D9719.15, NAA40, NAT11, PATT1 / Production host: ![]() References: UniProt: Q12306, UniProt: Q86UY6, N-terminal L-serine Nalpha-acetyltransferase NatD |
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| #55: Protein | Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861 |
+40S ribosomal protein ... , 23 types, 23 molecules SASBSCSDSESFSGSHSaSbScSfSjSkSlSmSoSpSuSvSxSySz
-Small ribosomal subunit protein ... , 6 types, 6 molecules SdSeSgSiStSw
| #44: Protein | Mass: 17654.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269 |
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| #45: Protein | Mass: 9150.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220 |
| #47: Protein | Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266 |
| #50: Protein | Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019 |
| #61: Protein | Mass: 32778.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865 |
| #64: Protein | Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701 |
-Non-polymers , 3 types, 12 molecules 




| #87: Chemical | ChemComp-ZN / #88: Chemical | ChemComp-COA / | #89: Chemical | ChemComp-GTP / | |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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| Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm |
| Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11206 / Symmetry type: POINT |
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About Yorodumi



Homo sapiens (human)

Brachypodium distachyon (stiff brome)
Switzerland,
Germany,
United States, 5items
Citation







PDBj































































FIELD EMISSION GUN