+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13134 | ||||||||||||
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Title | Structure of the hexameric 5S RNP from C. thermophilum | ||||||||||||
Map data | Hexameric 5S RNP from C. thermophilum | ||||||||||||
Sample |
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Keywords | 5S RNP / Ribosome biogenesis / Symportin 1 / Rpf2-Rrs1 / RNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information preribosome, large subunit precursor / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome ...preribosome, large subunit precursor / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / nucleolus / RNA binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Thermochaetoides thermophila DSM 1495 (fungus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Castillo N / Thoms M | ||||||||||||
Funding support | Germany, 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_13134.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-13134-v30.xml emd-13134.xml | 24.9 KB 24.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13134_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_13134.png | 68.3 KB | ||
Filedesc metadata | emd-13134.cif.gz | 6.8 KB | ||
Others | emd_13134_additional_1.map.gz emd_13134_additional_2.map.gz emd_13134_additional_3.map.gz emd_13134_additional_4.map.gz | 3 MB 5 MB 21.4 MB 21.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13134 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13134 | HTTPS FTP |
-Validation report
Summary document | emd_13134_validation.pdf.gz | 387.9 KB | Display | EMDB validaton report |
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Full document | emd_13134_full_validation.pdf.gz | 387.5 KB | Display | |
Data in XML | emd_13134_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_13134_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13134 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13134 | HTTPS FTP |
-Related structure data
Related structure data | 7ozsMC 8bguC 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_13134.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Hexameric 5S RNP from C. thermophilum | ||||||||||||||||||||
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: hexameric ct-sc 5S RNP monomer
File | emd_13134_additional_1.map | ||||||||||||
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Annotation | hexameric ct-sc 5S RNP monomer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: hexameric ct-sc 5S RNP dimer
File | emd_13134_additional_2.map | ||||||||||||
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Annotation | hexameric ct-sc 5S RNP dimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: pre-60S with human 5S RNP
File | emd_13134_additional_3.map | ||||||||||||
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Annotation | pre-60S with human 5S RNP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: human MDM2-5S RNP
File | emd_13134_additional_4.map | ||||||||||||
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Annotation | human MDM2-5S RNP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hexameric 5S RNP from C. thermophilum
Entire | Name: hexameric 5S RNP from C. thermophilum |
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Components |
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-Supramolecule #1: hexameric 5S RNP from C. thermophilum
Supramolecule | Name: hexameric 5S RNP from C. thermophilum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
-Macromolecule #1: Putative ribosomal protein
Macromolecule | Name: Putative ribosomal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 20.119275 KDa |
Sequence | String: MSSEKAQNPM RELRIQKLVL NISVGESGDR LTRAAKVLEQ LSGQTPVYSK ARYTVRQFGI RRNEKIAVHV TVRGPKAEEI LERGLKVKE YELRRRNFSE TGNFGFGISE HIDLGIKYDP SIGIYGMDFY CCMTRPGERV AKRRRCKSRI GASHRITREE T IRWFKQRF DGIVR UniProtKB: Putative ribosomal protein |
-Macromolecule #2: 60S ribosomal protein l5-like protein
Macromolecule | Name: 60S ribosomal protein l5-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 35.034605 KDa |
Sequence | String: MAFHKLVKNS AYYSRFQTKF KRRRQGKTDY YARKRLITQA KNKYNAPKYR LVVRFTNRDI ITQMVTSEIN GDKIFAAAYS HELRAYGIN HGLTNWAAAY ATGLLLARRV LAKLGLDKTF TGVEEPNGEY TLTEAAETED GERRPFKAIL DVGLARTSTG A RVFGVMKG ...String: MAFHKLVKNS AYYSRFQTKF KRRRQGKTDY YARKRLITQA KNKYNAPKYR LVVRFTNRDI ITQMVTSEIN GDKIFAAAYS HELRAYGIN HGLTNWAAAY ATGLLLARRV LAKLGLDKTF TGVEEPNGEY TLTEAAETED GERRPFKAIL DVGLARTSTG A RVFGVMKG ASDGGIFIPH SENRFPGYDI ETEELDTEVL KKYIYGGHVA EYMETLADDD EERYKSQFVK YIEDDVEADS LE ELYAEAH KQIRADPFRK YVSDAPKKSK EEWKAESLKY KKAKLSREER KARVEAKIKQ LLAEQDE UniProtKB: 60S ribosomal protein l5-like protein |
-Macromolecule #3: Ribosome biogenesis regulatory protein
Macromolecule | Name: Ribosome biogenesis regulatory protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 22.817281 KDa |
Sequence | String: MSTDTSKPAR LPVTVEKPTP YTFDLGLLLA NDPNPVNVPK TTDTQVLEQH LASVARDGAQ VLINQLLTTT TITATKDGVL LTLPPPTTP LPREKPVPQP KPETKWQAFA RRRGIKPKTR EQRRNLQYNP TTGQWERKWG YKGANKRGET DPIIEVSAAK E AMRPEGTS ...String: MSTDTSKPAR LPVTVEKPTP YTFDLGLLLA NDPNPVNVPK TTDTQVLEQH LASVARDGAQ VLINQLLTTT TITATKDGVL LTLPPPTTP LPREKPVPQP KPETKWQAFA RRRGIKPKTR EQRRNLQYNP TTGQWERKWG YKGANKRGET DPIIEVSAAK E AMRPEGTS VRGDKRREIR ARVKKNQKQM LRNQRIAAEK MGKK UniProtKB: Ribosome biogenesis regulatory protein |
-Macromolecule #4: Ribosome production factor 2 homolog
Macromolecule | Name: Ribosome production factor 2 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 39.92734 KDa |
Sequence | String: MLRQIKPRNA RSKRALEKRA PKIVENPKTC LFLRGTTCSQ ITQDAMNDLY AMRQVHAKRF HKKNAIHPFE DATSLCFFSE KNDCSLMVF GSSNKKRPHT LTFVRMFDYK VLDMLEFYLD PDTYRSISQF KTSKIPIGMR PMMVFAGTAF ESPVPNAFTM A KSMLIDFF ...String: MLRQIKPRNA RSKRALEKRA PKIVENPKTC LFLRGTTCSQ ITQDAMNDLY AMRQVHAKRF HKKNAIHPFE DATSLCFFSE KNDCSLMVF GSSNKKRPHT LTFVRMFDYK VLDMLEFYLD PDTYRSISQF KTSKIPIGMR PMMVFAGTAF ESPVPNAFTM A KSMLIDFF RGEPSDKIDV EGLRFVVVVT ADEPTSSTST NNDGENPAPL PGMTDPRSID PSQKPILRLR VYGIRTKRSG TR LPRVEVE EHGPRMDFRL GRMREPDPAM LKEAMKKAKT PQEERTKKNI SMDLLGDKIG RIHMGKTDLS KLQTRKMKGL KRG RDEDEG GEDDRTDVVE AGSGEKKKKK KVKG UniProtKB: Ribosome production factor 2 homolog |
-Macromolecule #6: unknown
Macromolecule | Name: unknown / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
Molecular weight | Theoretical: 1.975426 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) |
-Macromolecule #7: Syo1
Macromolecule | Name: Syo1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 74.709156 KDa |
Sequence | String: MGKTRRNRVR NRTDPIAKPV KPPTDPELAK LREDKILPVL KDLKSPDAKS RTTAAGAIAN IVQDAKCRKL LLREQVVHIV LTETLTDNN IDSRAAGWEI LKVLAQEEEA DFCVHLYRLD VLTAIEHAAK AVLETLTTSE PPFSKLLKAQ QRLVWDITGS L LVLIGLLA ...String: MGKTRRNRVR NRTDPIAKPV KPPTDPELAK LREDKILPVL KDLKSPDAKS RTTAAGAIAN IVQDAKCRKL LLREQVVHIV LTETLTDNN IDSRAAGWEI LKVLAQEEEA DFCVHLYRLD VLTAIEHAAK AVLETLTTSE PPFSKLLKAQ QRLVWDITGS L LVLIGLLA LARDEIHEAV ATKQTILRLL FRLISADIAP QDIYEEAISC LTTLSEDNLK VGQAITDDQE THVYDVLLKL AT GTDPRAV MACGVLHNVF TSLQWMDHSP GKDGACDAIL IPTLTRALEH VVPGGAKFNG DARYANITLL ALVTLASIGT DFQ ETLVKG NQGSRESPIS AADEEWNGFD DADGDAMDVD QKSSSGEDQE EDYEEIDVKE DDEDDDDDSI TSEMQADMER VVGA DGTDD GDLEDLPTLR ELIQTAVPQL IRLSNLPIDS DESLTIQSHA LSALNNISWT ISCLEFANGE NANIHNAWYP TAKKI WRKT ILPILEADSA DLKLATQVTS LAWAVARVLH GETPTDGNPH RKFISLYHSS KQQAGGNSNS IEEPEDPFQG LGVKCI GVV GSLAHDPAPI EVNREVGVFL VTLLRQSNNV PPAEIVEALN QLFDIYGDEE LACDKEVFWK DGFLKHLEEF LPKMRTL TK GIDKRTQPEL RTRADEALLN LGRFVQYKKK HAPK UniProtKB: ARM-like repeat-containing protein |
-Macromolecule #5: 5S rRNA
Macromolecule | Name: 5S rRNA / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 38.312738 KDa |
Sequence | String: ACGUACGACC AUACCCAGUG GAAAGCACGG CAUCCCGUCC GCUCUGCCCU AGUUAAGCCA CUGAGGGCCC GGUUAGUAGU UGGGUCGGU GACGACCAGC GAAUCCCGGG UGUUGUACGU |
-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 | Model: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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: 43.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |