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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 cytidine N-acetyltransferase activity / U6 snRNA 2'-O-ribose methyltransferase activity / nucleologenesis / oocyte growth / snoRNA localization / granular component / leucine zipper domain binding / tRNA wobble cytosine modification / U4atac snRNP / U4atac snRNA binding ...mRNA cytidine N-acetyltransferase activity / U6 snRNA 2'-O-ribose methyltransferase activity / nucleologenesis / oocyte growth / snoRNA localization / granular component / leucine zipper domain binding / tRNA wobble cytosine modification / U4atac snRNP / U4atac snRNA binding / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / regulation of stem cell population maintenance / tRNA acetylation / CURI complex / UTP-C complex / pre-snoRNP complex / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / box C/D sno(s)RNA binding / Mpp10 complex / negative regulation of amyloid precursor protein biosynthetic process / rRNA modification / rRNA (pseudouridine) methyltransferase activity / histone H2AQ104 methyltransferase activity / dense fibrillar component / histone methyltransferase binding / box C/D sno(s)RNA 3'-end processing / preribosome / rRNA methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription elongation by RNA polymerase II / regulation of centrosome duplication / N-acetyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cilium disassembly / box C/D methylation guide snoRNP complex / tRNA export from nucleus / positive regulation of rRNA processing / embryonic cleavage / RNA splicing, via transesterification reactions / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / blastocyst formation / rRNA base methylation / SUMOylation of RNA binding proteins / U2-type precatalytic spliceosome / protein localization to nucleolus / rRNA methylation / telomerase holoenzyme complex / transcription elongation factor activity / U4 snRNA binding / box C/D snoRNP assembly / spindle assembly involved in female meiosis / neural precursor cell proliferation / epigenetic programming in the zygotic pronuclei / protein acetylation / negative regulation of RNA splicing / U3 snoRNA binding / neural crest cell differentiation / NRAGE signals death through JNK / precatalytic spliceosome / snoRNA binding / preribosome, small subunit precursor / rRNA modification in the nucleus and cytosol / negative regulation of bicellular tight junction assembly / erythrocyte homeostasis / rRNA metabolic process / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / Cul4-RING E3 ubiquitin ligase complex / positive regulation of transcription by RNA polymerase I / Association of TriC/CCT with target proteins during biosynthesis / decidualization / negative regulation of telomere maintenance via telomerase / Ribosomal scanning and start codon recognition / Translation initiation complex formation / RNA polymerase II complex binding / TFIID-class transcription factor complex binding / Protein hydroxylation / negative regulation of apoptotic signaling pathway / TOR signaling / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / cellular response to ethanol / Peptide chain elongation / chromosome, centromeric region / Selenocysteine synthesis / Formation of a pool of free 40S subunits / single fertilization / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / 90S preribosome / Viral mRNA Translation
Similarity search - Function
Protein of unknown function DUF4602 / : / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / : / NUC129 domain / U3 small nucleolar RNA-associated protein 6 C-terminal / 40S small subunit processome assembly factor 1 / WD repeat-containing protein 75 first beta-propeller / Apoptosis-antagonizing transcription factor, C-terminal ...Protein of unknown function DUF4602 / : / Nucleolar protein 7, C-terminal / Rrp7A, RNA recognition motif / : / NUC129 domain / U3 small nucleolar RNA-associated protein 6 C-terminal / 40S small subunit processome assembly factor 1 / WD repeat-containing protein 75 first beta-propeller / 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 / Nucleolar protein 10-like, second domain / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH 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 / RNA cytidine acetyltransferase NAT10/TcmA, helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / : / WD repeat-containing protein 75 second beta-propeller / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Nrap protein domain 1 / 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 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / 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 domain / Nucleolar protein 10-like, N-terminal domain / Small subunit processome component 20 homolog, C-terminal / Sof1-like protein / : / Sof1-like domain / BING4, C-terminal domain / WD repeat-containing protein WDR46/Utp7 / BING4CT (NUC141) domain / BING4CT (NUC141) domain / U3 small nucleolar RNA-associated protein 6 / : / U3 small nucleolar RNA-associated protein 6 / rRNA-processing protein Fcf1, PIN domain / U3 small nucleolar RNA-associated protein 4 / Small-subunit processome, Utp11 / Fcf2 pre-rRNA processing, C-terminal / Fcf2/DNTTIP2 / : / Utp11 protein / Fcf2 pre-rRNA processing / rRNA-processing protein Fcf1/Utp23 / : / Fcf1 / U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / Small-subunit processome, Utp14 / Utp14 protein / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / BP28, C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / :
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 / 40S small subunit processome assembly factor 1 / 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
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  • 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
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 560 pix.
= 604.8 Å		1.08 Å/pix.
x 560 pix.
= 604.8 Å		1.08 Å/pix.
x 560 pix.
= 604.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
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

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Additional map: #1

Fileemd_23939_additional_1.map
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Half map: Half-Map1

Fileemd_23939_half_map_1.map
AnnotationHalf-Map1
Projections & Slices
AxesZYX

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Half map: Half-Map2

Fileemd_23939_half_map_2.map
AnnotationHalf-Map2
Projections & Slices
AxesZYX

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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
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 84904 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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)
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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