+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16036 | ||||||||||||
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Title | human MDM2-5S RNP | ||||||||||||
Map data | human MDM2-5S RNP (local filtered map) | ||||||||||||
Sample |
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Keywords | 5S RNP / Mdm2 / RNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / negative regulation of protein neddylation ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / negative regulation of protein neddylation / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / SUMO transferase activity / negative regulation of protein processing / response to iron ion / response to steroid hormone / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / endocardial cushion morphogenesis / negative regulation of ubiquitin protein ligase activity / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / Peptide chain elongation / ligase activity / Selenocysteine synthesis / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / response to magnesium ion / SUMOylation of transcription factors / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein sumoylation / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to UV-C / Major pathway of rRNA processing in the nucleolus and cytosol / blood vessel remodeling / cellular response to estrogen stimulus / protein targeting / protein autoubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to actinomycin D / ribonucleoprotein complex binding / cytosolic ribosome / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / negative regulation of ubiquitin-dependent protein catabolic process / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / positive regulation of protein export from nucleus / response to cocaine / proteolysis involved in protein catabolic process / regulation of signal transduction by p53 class mediator / ribosomal large subunit biogenesis / ubiquitin binding / mRNA 3'-UTR binding / positive regulation of translation / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / RING-type E3 ubiquitin transferase / establishment of protein localization / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / ribosomal large subunit assembly / response to toxic substance / cellular response to gamma radiation / cellular response to growth factor stimulus / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cellular response to hydrogen peroxide / protein polyubiquitination / rRNA processing / ubiquitin-protein transferase activity / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Castillo N / Thoms M / Flemming D / Hammaren HM / Buschauer R / Ameismeier M / Bassler J / Beck M / Beckmann R / Hurt E | ||||||||||||
Funding support | Germany, European Union, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways. Authors: Nestor Miguel Castillo Duque de Estrada / Matthias Thoms / Dirk Flemming / Henrik M Hammaren / Robert Buschauer / Michael Ameismeier / Jochen Baßler / Martin Beck / Roland Beckmann / Ed Hurt / Abstract: The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is ...The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is disturbed, a free 5S RNP can enter the MDM2-p53 pathway to regulate cell cycle and apoptotic signaling. Here we reconstitute and determine the cryo-electron microscopy structure of the conserved hexameric 5S RNP with fungal or human factors. This reveals how the nascent 5S rRNA associates with the initial nuclear import complex Syo1-uL18-uL5 and, upon further recruitment of the nucleolar factors Rpf2 and Rrs1, develops into the 5S RNP precursor that can assemble into the pre-ribosome. In addition, we elucidate the structure of another 5S RNP intermediate, carrying the human ubiquitin ligase Mdm2, which unravels how this enzyme can be sequestered from its target substrate p53. Our data provide molecular insight into how the 5S RNP can mediate between ribosome biogenesis and cell proliferation. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16036.map.gz | 21.1 MB | EMDB map data format | |
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Header (meta data) | emd-16036-v30.xml emd-16036.xml | 24.6 KB 24.6 KB | Display Display | EMDB header |
Images | emd_16036.png | 54.9 KB | ||
Others | emd_16036_additional_1.map.gz emd_16036_additional_2.map.gz emd_16036_additional_3.map.gz emd_16036_half_map_1.map.gz emd_16036_half_map_2.map.gz | 28.5 MB 23.2 MB 23.3 MB 23.4 MB 23.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16036 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16036 | HTTPS FTP |
-Validation report
Summary document | emd_16036_validation.pdf.gz | 610.1 KB | Display | EMDB validaton report |
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Full document | emd_16036_full_validation.pdf.gz | 609.6 KB | Display | |
Data in XML | emd_16036_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_16036_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16036 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16036 | HTTPS FTP |
-Related structure data
Related structure data | 8bguMC 7ozsC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16036.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | human MDM2-5S RNP (local filtered map) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: human MDM2-5S RNP (post-processed map)
File | emd_16036_additional_1.map | ||||||||||||
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Annotation | human MDM2-5S RNP (post-processed map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: human MDM2-5S RNP (maked 3D Refinement)
File | emd_16036_additional_2.map | ||||||||||||
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Annotation | human MDM2-5S RNP (maked 3D Refinement) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: human MDM2-5S RNP (unmaked 3D Refinement)
File | emd_16036_additional_3.map | ||||||||||||
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Annotation | human MDM2-5S RNP (unmaked 3D Refinement) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: human MDM2-5S RNP (maked 3D Refinement, half map 1)
File | emd_16036_half_map_1.map | ||||||||||||
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Annotation | human MDM2-5S RNP (maked 3D Refinement, half map 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: human MDM2-5S RNP (maked 3D Refinement, half map 2)
File | emd_16036_half_map_2.map | ||||||||||||
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Annotation | human MDM2-5S RNP (maked 3D Refinement, half map 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human MDM2-5S RNP
Entire | Name: human MDM2-5S RNP |
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Components |
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-Supramolecule #1: human MDM2-5S RNP
Supramolecule | Name: human MDM2-5S RNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: E3 ubiquitin-protein ligase Mdm2
Macromolecule | Name: E3 ubiquitin-protein ligase Mdm2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.293758 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MCNTNMSVPT DGAVTTSQIP ASEQETLVRP KPLLLKLLKS VGAQKDTYTM KEVLFYLGQY IMTKRLYDEK QQHIVYCSND LLGDLFGVP SFSVKEHRKI YTMIYRNLVV VNQQESSDSG TSVSENRCHL EGGSDQKDLV QELQEEKPSS SHLVSRPSTS S RRRAISET ...String: MCNTNMSVPT DGAVTTSQIP ASEQETLVRP KPLLLKLLKS VGAQKDTYTM KEVLFYLGQY IMTKRLYDEK QQHIVYCSND LLGDLFGVP SFSVKEHRKI YTMIYRNLVV VNQQESSDSG TSVSENRCHL EGGSDQKDLV QELQEEKPSS SHLVSRPSTS S RRRAISET EENSDELSGE RQRKRHKSDS ISLSFDESLA LCVIREICCE RSSSSESTGT PSNPDLDAGV SEHSGDWLDQ DS VSDQFSV EFEVESLDSE DYSLSEEGQE LSDEDDEVYQ VTVYQAGESD TDSFEEDPEI SLADYWKCTS CNEMNPPLPS HCN RCWALR ENWLPEDKGK DKGEISEKAK LENSTQAEEG FDVPDCKKTI VNDSRESCVE ENDDKITQAS QSQESEDYSQ PSTS SSIIY SSQEDVKEFE REETQDKEES VESSLPLNAI EPCVICQGRP KNGCIVHGKT GHLMACFTCA KKLKKRNKPC PVCRQ PIQM IVLTYFP UniProtKB: E3 ubiquitin-protein ligase Mdm2 |
-Macromolecule #3: 60S ribosomal protein L5
Macromolecule | Name: 60S ribosomal protein L5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.426789 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MGFVKVVKNK AYFKRYQVKF RRRREGKTDY YARKRLVIQD KNKYNTPKYR MIVRVTNRDI ICQIAYARIE GDMIVCAAYA HELPKYGVK VGLTNYAAAY CTGLLLARRL LNRFGMDKIY EGQVEVTGDE YNVESIDGQP GAFTCYLDAG LARTTTGNKV F GALKGAVD ...String: MGFVKVVKNK AYFKRYQVKF RRRREGKTDY YARKRLVIQD KNKYNTPKYR MIVRVTNRDI ICQIAYARIE GDMIVCAAYA HELPKYGVK VGLTNYAAAY CTGLLLARRL LNRFGMDKIY EGQVEVTGDE YNVESIDGQP GAFTCYLDAG LARTTTGNKV F GALKGAVD GGLSIPHSTK RFPGYDSESK EFNAEVHRKH IMGQNVADYM RYLMEEDEDA YKKQFSQYIK NSVTPDMMEE MY KKAHAAI RENPVYEKKP KKEVKKKRWN RPKMSLAQKK DRVAQKKASF LRAQERAAES UniProtKB: Large ribosomal subunit protein uL18 |
-Macromolecule #4: 60S ribosomal protein L11
Macromolecule | Name: 60S ribosomal protein L11 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 20.288465 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MAQDQGEKEN PMRELRIRKL CLNICVGESG DRLTRAAKVL EQLTGQTPVF SKARYTVRSF GIRRNEKIAV HCTVRGAKAE EILEKGLKV REYELRKNNF SDTGNFGFGI QEHIDLGIKY DPSIGIYGLD FYVVLGRPGF SIADKKRRTG CIGAKHRISK E EAMRWFQQ KYDGIILPGK UniProtKB: Large ribosomal subunit protein uL5 |
-Macromolecule #2: 5S rRNA
Macromolecule | Name: 5S rRNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 38.951105 KDa |
Sequence | String: GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGG UGACCAUACG CGAAACUCAG GUGCUGCAAU CU GENBANK: GENBANK: CP008196.1 |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219620 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |