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- EMDB-50968: snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 -

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Basic information

Entry
Database: EMDB / ID: EMD-50968
TitlesnR30 snoRNP - State 2 - Utp23-Krr1-deltaC3
Map datasnR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - local resolution filtered
Sample
  • Complex: Utp23-FTpA, Krr1-deltaC3
    • RNA: x 2 types
    • Protein or peptide: x 9 types
Keywords90S / pre-ribosome / snoRNA / snR30 / snoRNP / ribosome biogenesis / H/ACA / 18S rRNA / RIBOSOME
Function / homology
Function and homology information


snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups / snRNA pseudouridine synthesis / box H/ACA snoRNA binding ...snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups / snRNA pseudouridine synthesis / box H/ACA snoRNA binding / mRNA pseudouridine synthesis / pseudouridine synthase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / sno(s)RNA-containing ribonucleoprotein complex / telomerase RNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / snoRNA binding / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / chromosome, centromeric region / 90S preribosome / 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 SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / microtubule / cytoplasmic translation / structural constituent of ribosome / translation / cell division / mRNA binding / nucleolus / mitochondrion / DNA binding / RNA binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
KRR1 interacting protein 1 / Kri1-like, C-terminal / KRI1-like family / KRI1-like family C-terminal / UTP23 sensor motif / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like ...KRR1 interacting protein 1 / Kri1-like, C-terminal / KRI1-like family / KRI1-like family C-terminal / UTP23 sensor motif / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / Uncharacterised domain CHP00451 / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / PUA domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / Krr1, KH1 domain / Krr1 KH1 domain / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / PUA domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / K Homology domain, type 1 superfamily / PIN-like domain superfamily / PUA-like superfamily / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / K Homology domain / K homology RNA-binding domain / Ribosomal protein S15 signature. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / Ribosomal protein S11 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / KRR1 small subunit processome component / H/ACA ribonucleoprotein complex subunit GAR1 / H/ACA ribonucleoprotein complex subunit NHP2 / H/ACA ribonucleoprotein complex subunit CBF5 / Protein KRI1 / rRNA-processing protein UTP23 / H/ACA ribonucleoprotein complex subunit NOP10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsThoms M / Berninghausen O / Beckmann R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: Nat Commun / Year: 2025
Title: H/ACA snR30 snoRNP guides independent 18S rRNA subdomain formation.
Authors: Paulina Fischer / Matthias Thoms / Benjamin Lau / Timo Denk / Maria Kuvshinova / Otto Berninghausen / Dirk Flemming / Ed Hurt / Roland Beckmann /
Abstract: Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, ...Ribosome biogenesis follows a cascade of pre-rRNA folding and processing steps, coordinated with ribosomal protein incorporation. Nucleolar 90S pre-ribosomes are well-described stable intermediates, composed of pre-18S rRNA, ribosomal S-proteins, U3 snoRNA, and ~70 assembly factors. However, how numerous snoRNAs control pre-rRNA modification and folding during early maturation events remains unclear. We identify snR30 (human U17), the only essential H/ACA snoRNA in yeast, which binds with Cbf5-Gar1-Nop10-Nhp2 to a pre-18S rRNA subdomain containing platform helices and ES6 of the 40S central domain. Integration into the 90S is blocked by RNA hybridization with snR30. The snoRNP complex coordinates the recruitment of early assembly factors Krr1-Utp23-Kri1 and ribosomal proteins uS11-uS15, enabling isolated subdomain assembly. Krr1-dependent release of snR30 culminates in integration of the platform into the 90S. Our study reveals the essential role of snR30 in chaperoning central domain formation as a discrete assembly unit externalized from the pre-ribosomal core.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Adams PD
History
DepositionJul 10, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50968.png

Downloads & links

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Map

FileDownload / File: emd_50968.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationsnR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - local resolution filtered
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.9878992 - 3.371605
Average (Standard dev.)0.0036462757 (±0.061085004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - sharpened

Fileemd_50968_additional_1.map
AnnotationsnR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - sharpened
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Additional map: snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3

Fileemd_50968_additional_2.map
AnnotationsnR30 snoRNP - State 2 - Utp23-Krr1-deltaC3
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Half map: snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - half map A

Fileemd_50968_half_map_1.map
AnnotationsnR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - half map A
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Half map: snR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - half map B

Fileemd_50968_half_map_2.map
AnnotationsnR30 snoRNP - State 2 - Utp23-Krr1-deltaC3 - half map B
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Sample components

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Entire : Utp23-FTpA, Krr1-deltaC3

EntireName: Utp23-FTpA, Krr1-deltaC3
Components
  • Complex: Utp23-FTpA, Krr1-deltaC3
    • RNA: RDN18-1
    • RNA: snR30
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit CBF5
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit NOP10
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit GAR1
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit NHP2
    • Protein or peptide: KRR1 small subunit processome component
    • Protein or peptide: Protein KRI1
    • Protein or peptide: 40S ribosomal protein S13
    • Protein or peptide: 40S ribosomal protein S14-A
    • Protein or peptide: rRNA-processing protein UTP23

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Supramolecule #1: Utp23-FTpA, Krr1-deltaC3

SupramoleculeName: Utp23-FTpA, Krr1-deltaC3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: RDN18-1

MacromoleculeName: RDN18-1 / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 579.761938 KDa
SequenceString: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGUAUAAC UGUGGUAAUU C UAGAGCUA ...String:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGUAUAAC UGUGGUAAUU C UAGAGCUA AUACAUGCUU AAAAUCUCGA CCCUUUGGAA GAGAUGUAUU UAUUAGAUAA AAAAUCAAUG UCUUCGGACU CU UUGAUGA UUCAUAAUAA CUUUUCGAAU CGCAUGGCCU UGUGCUGGCG AUGGUUCAUU CAAAUUUCUG CCCUAUCAAC UUU CGAUGG UAGGAUAGUG GCCUACCAUG GUUUCAACGG GUAACGGGGA AUAAGGGUUC GAUUCCGGAG AGGGAGCCUG AGAA ACGGC UACCACAUCC AAGGAAGGCA GCAGGCGCGC AAAUUACCCA AUCCUAAUUC AGGGAGGUAG UGACAAUAAA UAACG AUAC AGGGCCCAUU CGGGUCUUGU AAUUGGAAUG AGUACAAUGU AAAUACCUUA ACGAGGAACA AUUGGAGGGC AAGUCU GGU GCCAGCAGCC GCGGUAAUUC CAGCUCCAAU AGCGUAUAUU AAAGUUGUUG CAGUUAAAAA GCUCGUAGUU GAACUUU GG GCCCGGUUGG CCGGUCCGAU UUUUUCGUGU ACUGGAUUUC CAACGGGGCC UUUCCUUCUG GCUAACCUUG AGUCCUUG U GGCUCUUGGC GAACCAGGAC UUUUACUUUG AAAAAAUUAG AGUGUUCAAA GCAGGCGUAU UGCUCGAAUA UAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUU CAAUUGUCAG AGGUGAAAUU CUUGGAUUUA UUGAAGACUA ACUACUGCGA AAGCAUUUGC CAAGGACGUU U UCAUUAAU CAAGAACGAA AGUUAGGGGA UCGAAGAUGA UCAGAUACCG UCGUAGUCUU AACCAUAAAC UAUGCCGACU AG GGAUCGG GUGGUGUUUU UUUAAUGACC CACUCGGCAC CUUACGAGAA AUCAAAGUCU UUGGGUUCUG GGGGGAGUAU GGU CGCAAG GCUGAAACUU AAAGGAAUUG ACGGAAGGGC ACCACCAGGA GUGGAGCCUG CGGCUUAAUU UGACUCAACA CGGG GAAAC UCACCAGGUC CAGACACAAU AAGGAUUGAC AGAUUGAGAG CUCUUUCUUG AUUUUGUGGG UGGUGGUGCA UGGCC GUUC UUAGUUGGUG GAGUGAUUUG UCUGCUUAAU UGCGAUAACG AACGAGACCU UAACCUACUA AAUAGUGGUG CUAGCA UUU GCUGGUUAUC CACUUCUUAG AGGGACUAUC GGUUUCAAGC CGAUGGAAGU UUGAGGCAAU AACAGGUCUG UGAUGCC CU UAGACGUUCU GGGCCGCACG CGCGCUACAC UGACGGAGCC AGCGAGUCUA ACCUUGGCCG AGAGGUCUUG GUAAUCUU G UGAAACUCCG UCGUGCUGGG GAUAGAGCAU UGUAAUUAUU GCUCUUCAAC GAGGAAUUCC UAGUAAGCGC AAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUA GAGAAGGGGG CAACUCCAUC UCAGAGCGGA GAAUUUGGAC AAACUUGGUC AUUUAGAGGA ACUAAAAGUC G UAACAAGG UUUCCGUAGG UGAACCUGCG GAAGGAUCAU UA

GENBANK: GENBANK: CP011558.1

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Macromolecule #2: snR30

MacromoleculeName: snR30 / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 195.416969 KDa
SequenceString: AACCAUAGUC UCGUGCUAGU UCGGUACUAU ACAGGGAAGG GAAGUCACUC GCAUACGUGU GUGUGCAUUU CUUGCUAUUG CUGCUUAGC UUCUCUAAAA CACUGGGCUA GCGUUUUUCA ACGCUCGAGA GGCAGAGUCU CAAGGAGCCU CCAAUGGGCC U CACGUAUU ...String:
AACCAUAGUC UCGUGCUAGU UCGGUACUAU ACAGGGAAGG GAAGUCACUC GCAUACGUGU GUGUGCAUUU CUUGCUAUUG CUGCUUAGC UUCUCUAAAA CACUGGGCUA GCGUUUUUCA ACGCUCGAGA GGCAGAGUCU CAAGGAGCCU CCAAUGGGCC U CACGUAUU CAUCUAGAUG GCGCUUCGGA CAACGGCAUC ACAUAAGAGA UGCAGCUCCU GACUUCUCCU CUGAUCUUCG UG AUCAGAG UUUUGAGUCG UCAGACUACG AGCAGUUUCU CUUAGUCGUU GCAUCGGGUG CUGUUGCCUU AACGAUGUGU AUA UGGGGU UCGGGGGCUG UUGCCAUGAU AUAUAUGGAU GAGACAGAAG UGGCCCCGUU GACGAGUUUA ACUUAGAUUA AGUA GGACG CAUGAUCUUG AGCUCUUUUC CUAUACUUUG UCCUAUGGCC AGCUUUCUCC UUAUUACGAA GAGAUUGCGG GAUGU GGGU GCAGAGUGGG AAAAUCUGAG UUCGGUCAUC UUUGUUGUUC GUCCUACCGC AGUAUAUUCC UAAACACUAU GAAAUG ACC CUAGUUGGUC CAUGAUCAUU UGGGUAAAAC CAUACUGCAG ACAUCU

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Macromolecule #3: H/ACA ribonucleoprotein complex subunit CBF5

MacromoleculeName: H/ACA ribonucleoprotein complex subunit CBF5 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Isomerases; Intramolecular transferases; Transferring other groups
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 54.804965 KDa
SequenceString: MSKEDFVIKP EAAGASTDTS EWPLLLKNFD KLLVRSGHYT PIPAGSSPLK RDLKSYISSG VINLDKPSNP SSHEVVAWIK RILRCEKTG HSGTLDPKVT GCLIVCIDRA TRLVKSQQGA GKEYVCIVRL HDALKDEKDL GRSLENLTGA LFQRPPLISA V KRQLRVRT ...String:
MSKEDFVIKP EAAGASTDTS EWPLLLKNFD KLLVRSGHYT PIPAGSSPLK RDLKSYISSG VINLDKPSNP SSHEVVAWIK RILRCEKTG HSGTLDPKVT GCLIVCIDRA TRLVKSQQGA GKEYVCIVRL HDALKDEKDL GRSLENLTGA LFQRPPLISA V KRQLRVRT IYESNLIEFD NKRNLGVFWA SCEAGTYMRT LCVHLGMLLG VGGHMQELRR VRSGALSEND NMVTLHDVMD AQ WVYDNTR DESYLRSIIQ PLETLLVGYK RIVVKDSAVN AVCYGAKLMI PGLLRYEEGI ELYDEIVLIT TKGEAIAVAI AQM STVDLA SCDHGVVASV KRCIMERDLY PRRWGLGPVA QKKKQMKADG KLDKYGRVNE NTPEQWKKEY VPLDNAEQST SSSQ ETKET EEEPKKAKED SLIKEVETEK EEVKEDDSKK EKKEKKDKKE KKEKKEKKDK KEKKEKKEKK RKSEDGDSEE KKSKK SKK

UniProtKB: H/ACA ribonucleoprotein complex subunit CBF5

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Macromolecule #4: H/ACA ribonucleoprotein complex subunit NOP10

MacromoleculeName: H/ACA ribonucleoprotein complex subunit NOP10 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.649745 KDa
SequenceString:
MHLMYTLGPD GKRIYTLKKV TESGEITKSA HPARFSPDDK YSRQRVTLKK RFGLVPGQ

UniProtKB: H/ACA ribonucleoprotein complex subunit NOP10

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Macromolecule #5: H/ACA ribonucleoprotein complex subunit GAR1

MacromoleculeName: H/ACA ribonucleoprotein complex subunit GAR1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.520441 KDa
SequenceString: MSFRGGNRGG RGGFRGGFRG GRTGSARSFQ QGPPDTVLEM GAFLHPCEGD IVCRSINTKI PYFNAPIYLE NKTQVGKVDE ILGPLNEVF FTIKCGDGVQ ATSFKEGDKF YIAADKLLPI ERFLPKPKVV GPPKPKNKKK RSGAPGGRGG ASMGRGGSRG G FRGGRGGS ...String:
MSFRGGNRGG RGGFRGGFRG GRTGSARSFQ QGPPDTVLEM GAFLHPCEGD IVCRSINTKI PYFNAPIYLE NKTQVGKVDE ILGPLNEVF FTIKCGDGVQ ATSFKEGDKF YIAADKLLPI ERFLPKPKVV GPPKPKNKKK RSGAPGGRGG ASMGRGGSRG G FRGGRGGS SFRGGRGGSS FRGGSRGGSF RGGSRGGSRG GFRGGRR

UniProtKB: H/ACA ribonucleoprotein complex subunit GAR1

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Macromolecule #6: H/ACA ribonucleoprotein complex subunit NHP2

MacromoleculeName: H/ACA ribonucleoprotein complex subunit NHP2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.158062 KDa
SequenceString:
MGKDNKEHKE SKESKTVDNY EARMPAVLPF AKPLASKKLN KKVLKTVKKA SKAKNVKRGV KEVVKALRKG EKGLVVIAGD ISPADVISH IPVLCEDHSV PYIFIPSKQD LGAAGATKRP TSVVFIVPGS NKKKDGKNKE EEYKESFNEV VKEVQAL

UniProtKB: H/ACA ribonucleoprotein complex subunit NHP2

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Macromolecule #7: KRR1 small subunit processome component

MacromoleculeName: KRR1 small subunit processome component / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.226254 KDa
SequenceString: MVSTHNRDKP WDTDDIDKWK IEEFKEEDNA SGQPFAEESS FMTLFPKYRE SYLKTIWNDV TRALDKHNIA CVLDLVEGSM TVKTTRKTY DPAIILKARD LIKLLARSVP FPQAVKILQD DMACDVIKIG NFVTNKERFV KRRQRLVGPN GNTLKALELL T KCYILVQG ...String:
MVSTHNRDKP WDTDDIDKWK IEEFKEEDNA SGQPFAEESS FMTLFPKYRE SYLKTIWNDV TRALDKHNIA CVLDLVEGSM TVKTTRKTY DPAIILKARD LIKLLARSVP FPQAVKILQD DMACDVIKIG NFVTNKERFV KRRQRLVGPN GNTLKALELL T KCYILVQG NTVSAMGPFK GLKEVRRVVE DCMKNIHPIY HIKELMIKRE LAKRPELANE DWSRFLPMFK KRNVARKKPK KI RNVEKKV YTPFPPAQLP RKVDLEIESG EYFLSKREKQ MKKLNEQKEK QMEREIERQE ERAKDFIAPE EEAYKPNQN

UniProtKB: KRR1 small subunit processome component

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Macromolecule #8: Protein KRI1

MacromoleculeName: Protein KRI1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 68.778961 KDa
SequenceString: MPRKKSAAKR AREQAKKEAA VPATDTATIK TSETSATTVK PAIEASKSYV PSEDEEEDEE EEEEEDDYGE LITDEVENGI NQVLDAIKN NKTDKLLDPK VKFFEDPESA AAKLANREGK HKPIYLKDYH RMNILSGDAL KEDDEEYEHA TVDGKQSFVS Q QREEKTQL ...String:
MPRKKSAAKR AREQAKKEAA VPATDTATIK TSETSATTVK PAIEASKSYV PSEDEEEDEE EEEEEDDYGE LITDEVENGI NQVLDAIKN NKTDKLLDPK VKFFEDPESA AAKLANREGK HKPIYLKDYH RMNILSGDAL KEDDEEYEHA TVDGKQSFVS Q QREEKTQL LNEIKSAFSD EENEESSGDE DDGFLKKKEP STKKEGKNLP DPTVNEENFL EEFVNQQAWI PKKGDKVISL DL NNNEEDD EEFEDAAEKF ENAYNFRYED PNAAEIISYA RSQATLRRSD DSSRRRKREE KRKIKEQIKA EKETALQKKK TKK LNKLTD ILEQLTKEYG AEINADMVKK ITDTLLKNDF KEEEWDNVVA ELFNEEFYQQ EGKPTWNEDD EIMGDFYADA DGDD QTEEG EVEKEQKEED EEEGPKRKKS KKEEKLQKKK EKRKVNELVE NALEQNKLAL IEEVEKEEEE RKSRSRTKEE QDLKF RYRE VSPESFGLTA REIFAADDTD LNEFIGLKKF APYRSKELRA KDKRKVMKAR RLREWRKKTF KNENGLAPVE AEAGEK DED TILIPVEKAS KSKHKRGHSH KHKGHQKK

UniProtKB: Protein KRI1

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Macromolecule #9: 40S ribosomal protein S13

MacromoleculeName: 40S ribosomal protein S13 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.059945 KDa
SequenceString:
MGRMHSAGKG ISSSAIPYSR NAPAWFKLSS ESVIEQIVKY ARKGLTPSQI GVLLRDAHGV TQARVITGNK IMRILKSNGL APEIPEDLY YLIKKAVSVR KHLERNRKDK DAKFRLILIE SRIHRLARYY RTVAVLPPNW KYESATASAL VN

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #10: 40S ribosomal protein S14-A

MacromoleculeName: 40S ribosomal protein S14-A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.562655 KDa
SequenceString:
MSNVVQARDN SQVFGVARIY ASFNDTFVHV TDLSGKETIA RVTGGMKVKA DRDESSPYAA MLAAQDVAAK CKEVGITAVH VKIRATGGT RTKTPGPGGQ AALRALARSG LRIGRIEDVT PVPSDSTRKK GGRRGRRL

UniProtKB: Small ribosomal subunit protein uS11A

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Macromolecule #11: rRNA-processing protein UTP23

MacromoleculeName: rRNA-processing protein UTP23 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.859338 KDa
SequenceString: MRQKRAKSYR KQLLVYSHTF KFREPYQVLV DNQLVLECNN SNFNLPSGLK RTLQADVKVM ITQCCIQALY ETRNDGAINL AKQFERRRC NHSFKDPKSP AECIESVVNI SGANKHRYVV ASQDIDLRRK LRTVPGVPLI HLTRSVMVME PLSTASAKAS K ITEEQKLY ...String:
MRQKRAKSYR KQLLVYSHTF KFREPYQVLV DNQLVLECNN SNFNLPSGLK RTLQADVKVM ITQCCIQALY ETRNDGAINL AKQFERRRC NHSFKDPKSP AECIESVVNI SGANKHRYVV ASQDIDLRRK LRTVPGVPLI HLTRSVMVME PLSTASAKAS K ITEEQKLY KGLNDPNIEK LQESGDGSGK ESITKKRKLG PKAPNPLSVK KKKKVNSPSD EVKDKEDTSK EKKKRRRRKH KS NTNVPVS NGTTAAQ

UniProtKB: rRNA-processing protein UTP23

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67293
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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