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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 data
SampleHuman SSU processome, state pre-A1
Function / homology
Function and homology information


mRNA N-acetyltransferase activity / nucleologenesis / preribosome / U4atac snRNP / snoRNA localization / rRNA acetylation involved in maturation of SSU-rRNA / U4atac snRNA binding / negative regulation of superoxide anion generation / rRNA cytidine N-acetyltransferase activity / transcription elongation regulator activity ...mRNA N-acetyltransferase activity / nucleologenesis / preribosome / U4atac snRNP / snoRNA localization / rRNA acetylation involved in maturation of SSU-rRNA / U4atac snRNA binding / negative regulation of superoxide anion generation / rRNA cytidine N-acetyltransferase activity / transcription elongation regulator activity / tRNA acetylation / CURI complex / regulation of transcription elongation from RNA polymerase II promoter / t-UTP complex / UTP-C complex / negative regulation of amyloid precursor protein biosynthetic process / Pwp2p-containing subcomplex of 90S preribosome / histone-glutamine methyltransferase activity / box C/D RNA binding / box C/D RNA 3'-end processing / leucine zipper domain binding / regulation of stem cell population maintenance / Mpp10 complex / pre-snoRNP complex / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / negative regulation of phosphatase activity / positive regulation of rRNA processing / regulation of centrosome duplication / rRNA modification / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / dense fibrillar component / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / embryonic cleavage / histone methyltransferase binding / blastocyst formation / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mammalian oogenesis stage / RNA splicing, via transesterification reactions / rRNA primary transcript binding / box C/D RNP complex / positive regulation of transcription by RNA polymerase I / negative regulation of RNA splicing / rRNA base methylation / ubiquitin ligase inhibitor activity / telomerase holoenzyme complex / cytoplasmic side of rough endoplasmic reticulum membrane / U2-type precatalytic spliceosome / rRNA modification in the nucleus and cytosol / activation-induced cell death of T cells / sno(s)RNA-containing ribonucleoprotein complex / response to stimulus / histone glutamine methylation / U4 snRNA binding / negative regulation of ubiquitin protein ligase activity / SUMOylation of RNA binding proteins / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / blastocyst development / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / negative regulation of telomere maintenance via telomerase / intercellular bridge / Ribosomal scanning and start codon recognition / tRNA export from nucleus / Translation initiation complex formation / translation regulator activity / 90S preribosome / preribosome, small subunit precursor / TFIID-class transcription factor complex binding / mRNA Splicing - Minor Pathway / precatalytic spliceosome / regulation of mitotic cell cycle / erythrocyte development / Peptide chain elongation / Association of TriC/CCT with target proteins during biosynthesis / NRAGE signals death through JNK / TOR signaling / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / RNA polymerase II complex binding / snoRNA binding / mTORC1-mediated signalling / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / rRNA methylation / Response of EIF2AK4 (GCN2) to amino acid deficiency / T cell proliferation involved in immune response / poly(U) RNA binding / N-acetyltransferase activity / stress granule assembly / Viral mRNA Translation / protein acetylation / GTP hydrolysis and joining of the 60S ribosomal subunit / 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) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Major pathway of rRNA processing in the nucleolus and cytosol / L13a-mediated translational silencing of Ceruloplasmin expression / GABA-ergic synapse
Similarity search - Function
Protein of unknown function DUF4602 / NUC129 domain / Nucleolar protein 7 / Rrp7A, RNA recognition motif / Nucleolar protein 7, C-terminal / 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 / NUC129 domain / Nucleolar protein 7 / Rrp7A, RNA recognition motif / Nucleolar protein 7, C-terminal / 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 / NUC153 domain / Nucleolar protein 10/Enp2 / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Possible tRNA binding domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase domain / GNAT acetyltransferase 2 / Helicase / Domain of unknown function (DUF1726) / Ribosomal RNA assembly KRR1 / Down-regulated-in-metastasis protein / Down-regulated in metastasis / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / rRNA-processing protein Fcf1, PIN domain / Fcf2 pre-rRNA processing / Nrap protein domain 1 / Small-subunit processome, Utp11 / Nrap protein, domain 6 / Utp11 protein / Nrap protein domain 1 / Fcf2 pre-rRNA processing, C-terminal / Nrap protein, domain 2 / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Sof1-like protein / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein PAP/OAS1-like domain 5 / NOL6/Upt22 / Nrap protein domain 6 / BING4, C-terminal domain / BING4CT (NUC141) domain / Fcf2/DNTTIP2 / Sof1-like domain / Nrap protein, domain 5 / BING4CT (NUC141) domain / WD repeat-containing protein WDR46/Utp7 / Nrap protein PAP/OAS-like domain / Ribosomal RNA-processing protein 7 / U3 small nucleolar RNA-associated protein 6 / Rrp7 RRM-like N-terminal domain / Ribosomal RNA-processing protein 7, C-terminal domain / Fcf1 / U3 small nucleolar RNA-associated protein 15, C-terminal / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / rRNA-processing protein Fcf1/Utp23 / UTP15 C terminal / Rrp7, RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 6 / Small-subunit processome, Utp14 / Sas10 C-terminal domain / Sas10 C-terminal domain / NOP5NT (NUC127) domain / NOP5, N-terminal / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / Periodic tryptophan protein 2 / Krr1 KH1 domain / Utp13 specific WD40 associated domain / Small-subunit processome, Utp13 / Krr1, KH1 domain / Sas10/Utp3/C1D family / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 10, N-terminal / Sas10/Utp3/C1D / BP28CT (NUC211) domain / BP28, C-terminal domain / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Ribosomal RNA-processing protein Rrp9-like / Small-subunit processome, Utp21 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Pre-rRNA-processing protein PNO1-like / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase domain superfamily
Similarity search - Domain/homology
Nucleolar protein 6 / 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 ...Nucleolar protein 6 / 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 / RNA 3'-terminal phosphate cyclase-like protein / 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 / Nucleolar protein 7 / WD repeat-containing protein 3 / Deoxynucleotidyltransferase terminal-interacting protein 2 / Nucleolar protein 58 / rRNA-processing protein FCF1 homolog / Probable U3 small nucleolar RNA-associated protein 11 / Ribosomal RNA-processing protein 7 homolog A / WD repeat-containing protein 75 / 40S ribosomal protein S13 / Periodic tryptophan protein 2 homolog / 40S ribosomal protein S3a / 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 / 40S ribosomal protein S17 / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S12 / 40S ribosomal protein S27 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / NHP2-like protein 1 / 40S ribosomal protein S7 / WD repeat-containing protein 43 / 40S ribosomal protein S8 / 40S ribosomal protein S15a / 40S ribosomal protein S16 / 40S ribosomal protein S14 / 40S ribosomal protein S23 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S24 / 40S ribosomal protein S28 / Transducin beta-like protein 3 / KRR1 small subunit processome component homolog / 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: [Figure: see text].
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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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Segmentation: #1

Fileemd_23939_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_23939_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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

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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

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Sample components

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Entire Human SSU processome, state pre-A1

EntireName: Human SSU processome, state pre-A1 / Number of Components: 1

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Component #1: protein, Human SSU processome, state pre-A1

ProteinName: Human SSU processome, state pre-A1 / Recombinant expression: No
MassTheoretical: 5 MDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 283 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 58 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 0.01 mm / Imaging Mode: BRIGHT FIELD / Defocus: 700.0 - 2700.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of Digital Images: 84904

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 42142
3D reconstructionSoftware: RELION / Resolution: 3.51 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL

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