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- EMDB-13134: Structure of the hexameric 5S RNP from C. thermophilum -

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Basic information

Entry
Database: EMDB / ID: EMD-13134
TitleStructure of the hexameric 5S RNP from C. thermophilum
Map dataHexameric 5S RNP from C. thermophilum
Sample
  • Complex: hexameric 5S RNP from C. thermophilum
    • Protein or peptide: Putative ribosomal protein
    • Protein or peptide: 60S ribosomal protein l5-like protein
    • Protein or peptide: Ribosome biogenesis regulatory protein
    • Protein or peptide: Ribosome production factor 2 homolog
    • RNA: 5S rRNA
    • Protein or peptide: unknown
    • Protein or peptide: Syo1
Keywords5S RNP / Ribosome biogenesis / Symportin 1 / Rpf2-Rrs1 / RNA BINDING PROTEIN
Function / homology
Function and homology information


ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein import into nucleus / unfolded protein binding / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome ...ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein import into nucleus / unfolded protein binding / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / nucleolus / nucleus
Similarity search - Function
: / Ribosome biogenesis protein Rpf2 / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Brix domain / Brix domain / Brix domain profile. / Brix / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region ...: / Ribosome biogenesis protein Rpf2 / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Brix domain / Brix domain / Brix domain profile. / Brix / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Armadillo-like helical / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Symportin 1 / Ribosome biogenesis regulatory protein homolog / Large ribosomal subunit protein uL18 / Ribosome production factor 2 homolog / Large ribosomal subunit protein uL5
Similarity search - Component
Biological speciesChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Thermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCastillo N / Thoms M
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)RK1721 Germany
German Research Foundation (DFG)HU363/15-2 Germany
European Research Council (ERC)885711 Germany
CitationJournal: 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
DepositionJun 28, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13134.png

Downloads & links

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Map

FileDownload / File: emd_13134.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHexameric 5S RNP from C. thermophilum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.16 Å		1.06 Å/pix.
x 240 pix.
= 254.16 Å		1.06 Å/pix.
x 240 pix.
= 254.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.0151511 - 2.7336893
Average (Standard dev.)0.0133727975 (±0.08340236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: hexameric ct-sc 5S RNP monomer

Fileemd_13134_additional_1.map
Annotationhexameric ct-sc 5S RNP monomer
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: hexameric ct-sc 5S RNP dimer

Fileemd_13134_additional_2.map
Annotationhexameric ct-sc 5S RNP dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: pre-60S with human 5S RNP

Fileemd_13134_additional_3.map
Annotationpre-60S with human 5S RNP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: human MDM2-5S RNP

Fileemd_13134_additional_4.map
Annotationhuman MDM2-5S RNP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : hexameric 5S RNP from C. thermophilum

EntireName: hexameric 5S RNP from C. thermophilum
Components
  • Complex: hexameric 5S RNP from C. thermophilum
    • Protein or peptide: Putative ribosomal protein
    • Protein or peptide: 60S ribosomal protein l5-like protein
    • Protein or peptide: Ribosome biogenesis regulatory protein
    • Protein or peptide: Ribosome production factor 2 homolog
    • RNA: 5S rRNA
    • Protein or peptide: unknown
    • Protein or peptide: Syo1

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Supramolecule #1: hexameric 5S RNP from C. thermophilum

SupramoleculeName: hexameric 5S RNP from C. thermophilum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Macromolecule #1: Putative ribosomal protein

MacromoleculeName: Putative ribosomal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 20.119275 KDa
SequenceString:
MSSEKAQNPM RELRIQKLVL NISVGESGDR LTRAAKVLEQ LSGQTPVYSK ARYTVRQFGI RRNEKIAVHV TVRGPKAEEI LERGLKVKE YELRRRNFSE TGNFGFGISE HIDLGIKYDP SIGIYGMDFY CCMTRPGERV AKRRRCKSRI GASHRITREE T IRWFKQRF DGIVR

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #2: 60S ribosomal protein l5-like protein

MacromoleculeName: 60S ribosomal protein l5-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 35.034605 KDa
SequenceString: 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: Large ribosomal subunit protein uL18

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Macromolecule #3: Ribosome biogenesis regulatory protein

MacromoleculeName: Ribosome biogenesis regulatory protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 22.817281 KDa
SequenceString: 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 homolog

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Macromolecule #4: Ribosome production factor 2 homolog

MacromoleculeName: Ribosome production factor 2 homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 39.92734 KDa
SequenceString: 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

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Macromolecule #6: unknown

MacromoleculeName: unknown / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Molecular weightTheoretical: 1.975426 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #7: Syo1

MacromoleculeName: Syo1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 74.709156 KDa
SequenceString: 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: Symportin 1

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Macromolecule #5: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 38.312738 KDa
SequenceString:
ACGUACGACC AUACCCAGUG GAAAGCACGG CAUCCCGUCC GCUCUGCCCU AGUUAAGCCA CUGAGGGCCC GGUUAGUAGU UGGGUCGGU GACGACCAGC GAAUCCCGGG UGUUGUACGU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126547
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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