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- EMDB-23939: Cryo-EM structure of the human SSU processome, state pre-A1 - raw maps -

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Basic information

Entry
Database: EMDB / ID: EMD-23939
TitleCryo-EM structure of the human SSU processome, state pre-A1 - raw maps
Map dataMain map
Sample
  • Complex: Human SSU processome, state pre-A1
Function / homology
Function and homology information


mRNA N-acetyltransferase activity / negative regulation of superoxide anion generation / preribosome / oocyte growth / nucleologenesis / U4atac snRNP / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / snoRNA localization / leucine zipper domain binding ...mRNA N-acetyltransferase activity / negative regulation of superoxide anion generation / preribosome / oocyte growth / nucleologenesis / U4atac snRNP / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / snoRNA localization / leucine zipper domain binding / granular component / U4atac snRNA binding / tRNA acetylation / t-UTP complex / CURI complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / regulation of stem cell population maintenance / negative regulation of amyloid precursor protein biosynthetic process / box C/D sno(s)RNA binding / histone H2AQ104 methyltransferase activity / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / dense fibrillar component / pre-snoRNP complex / rRNA modification / regulation of transcription elongation by RNA polymerase II / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of centrosome duplication / rRNA methyltransferase activity / histone methyltransferase binding / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / embryonic cleavage / rRNA base methylation / transcription elongation factor activity / epigenetic programming in the zygotic pronuclei / RNA splicing, via transesterification reactions / blastocyst formation / spindle assembly involved in female meiosis / rRNA primary transcript binding / cilium disassembly / negative regulation of RNA splicing / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / Cul4-RING E3 ubiquitin ligase complex / telomerase holoenzyme complex / U2-type precatalytic spliceosome / protein localization to nucleolus / box C/D snoRNP assembly / SUMOylation of RNA binding proteins / N-acetyltransferase activity / negative regulation of telomere maintenance via telomerase / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / rRNA methylation / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / response to stimulus / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / ubiquitin ligase inhibitor activity / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / precatalytic spliceosome / preribosome, small subunit precursor / Translation initiation complex formation / snoRNA binding / intercellular bridge / NRAGE signals death through JNK / positive regulation of transcription by RNA polymerase I / RNA polymerase II complex binding / protein acetylation / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / single fertilization / 90S preribosome / mTORC1-mediated signalling / Association of TriC/CCT with target proteins during biosynthesis / Peptide chain elongation / regulation of mitotic cell cycle / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / TFIID-class transcription factor complex binding / blastocyst development / negative regulation of apoptotic signaling pathway / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / ubiquitin-like ligase-substrate adaptor activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Viral mRNA Translation / chromosome, centromeric region / decidualization
Similarity search - Function
Protein of unknown function DUF4602 / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / Nucleolar protein 7 / NUC129 domain / Domain of unknown function (DUF4602) / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / Apoptosis-antagonizing transcription factor, C-terminal ...Protein of unknown function DUF4602 / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / Nucleolar protein 7 / NUC129 domain / Domain of unknown function (DUF4602) / Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / NUC153 / Nucleolar protein 10/Enp2 / NUC153 domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Ribosomal RNA assembly KRR1 / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20, C-terminal / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 small nucleolar RNA-associated protein 20, C-terminal / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / U3 small nucleolar RNA-associated protein 6 / rRNA-processing protein Fcf1, PIN domain / U3 small nucleolar RNA-associated protein 6 / NOL6/Upt22 / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Ribosomal RNA-processing protein Rrp9-like / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 / Nrap protein domain 1 / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / BING4CT (NUC141) domain / rRNA-processing protein Fcf1/Utp23 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Fcf1 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Small-subunit processome, Utp14 / U3 small nucleolar RNA-associated protein 15, C-terminal / Utp14 protein / UTP15 C terminal / Sas10 C-terminal domain / Sas10 C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Sas10/Utp3/C1D / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / Mpp10 protein / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily
Similarity search - Domain/homology
U3 small nucleolar ribonucleoprotein protein MPP10 / Nucleolar protein 56 / WD repeat-containing protein 46 / U3 small nucleolar RNA-interacting protein 2 / Small subunit processome component 20 homolog / Small ribosomal subunit protein eS17 / rRNA 2'-O-methyltransferase fibrillarin / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 ...U3 small nucleolar ribonucleoprotein protein MPP10 / Nucleolar protein 56 / WD repeat-containing protein 46 / U3 small nucleolar RNA-interacting protein 2 / Small subunit processome component 20 homolog / Small ribosomal subunit protein eS17 / rRNA 2'-O-methyltransferase fibrillarin / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / NHP2-like protein 1 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS28 / Transducin beta-like protein 3 / KRR1 small subunit processome component homolog / WD repeat-containing protein 43 / Periodic tryptophan protein 2 homolog / Deoxynucleotidyltransferase terminal-interacting protein 2 / WD repeat-containing protein 75 / Uncharacterized protein C1orf131 / Neuroguidin / WD repeat-containing protein 36 / U3 small nucleolar RNA-associated protein 15 homolog / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 4 homolog / U3 small nucleolar ribonucleoprotein protein IMP4 / Nucleolar protein 10 / U3 small nucleolar RNA-associated protein 14 homolog A / RNA cytidine acetyltransferase / HEAT repeat-containing protein 1 / Nucleolar protein 6 / Something about silencing protein 10 / RNA-binding protein PNO1 / DDB1- and CUL4-associated factor 13 / U3 small nucleolar ribonucleoprotein protein IMP3 / Protein AATF / U3 small nucleolar RNA-associated protein 6 homolog / U3 small nucleolar RNA-associated protein NOL7 / WD repeat-containing protein 3 / RNA 3'-terminal phosphate cyclase-like protein / Nucleolar protein 58 / rRNA-processing protein FCF1 homolog / Probable U3 small nucleolar RNA-associated protein 11 / Ribosomal RNA-processing protein 7 homolog A / U3 small nucleolar RNA-associated protein 18 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsVanden Broeck A / Singh S / Klinge S
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
European Molecular Biology Organization (EMBO)ALTF 711-2019
CitationJournal: Science / Year: 2021
Title: Nucleolar maturation of the human small subunit processome.
Authors: Sameer Singh / Arnaud Vanden Broeck / Linamarie Miller / Malik Chaker-Margot / Sebastian Klinge /
Abstract: The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution ...The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. These structures reveal the molecular mechanisms that enable crucial progressions during SSU processome maturation. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding. These conserved mechanisms highlight the SSU processome’s impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within.
History
DepositionMay 5, 2021-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateSep 29, 2021-
Current statusSep 29, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0061
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0061
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23939.png

Downloads & links

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Map

FileDownload / File: emd_23939.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0061 / Movie #1: 0.0061
Minimum - Maximum-0.045335583 - 0.099228285
Average (Standard dev.)0.0003968029 (±0.002331629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 604.80005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z604.800604.800604.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0450.0990.000

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Supplemental data

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Mask #1

Fileemd_23939_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_23939_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-Map1

Fileemd_23939_half_map_1.map
AnnotationHalf-Map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-Map2

Fileemd_23939_half_map_2.map
AnnotationHalf-Map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human SSU processome, state pre-A1

EntireName: Human SSU processome, state pre-A1
Components
  • Complex: Human SSU processome, state pre-A1

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Supramolecule #1: Human SSU processome, state pre-A1

SupramoleculeName: Human SSU processome, state pre-A1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5 MDa

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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: 7.6
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 84904 / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9297626
CTF correctionSoftware - Name: Gctf (ver. v1.06)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 42142
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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