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- EMDB-66688: Cryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut) from C... -

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Basic information

Entry
Database: EMDB / ID: EMD-66688
TitleCryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum, state Tsr1-1*
Map datalocal resolution filtered using Relion
Sample
  • Complex: pre-40S ribosome, state Tsr1-1*
    • Protein or peptide: x 18 types
    • RNA: x 1 types
  • Ligand: x 3 types
Keywords90S pre-ribosome / Rrp12 / Enp1 / ribosome biogenesis / RIBOSOME
Function / homology
Function and homology information


rRNA (guanine-N7)-methylation / rRNA (guanine) methyltransferase activity / 90S preribosome / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / methyltransferase activity / small-subunit processome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit ...rRNA (guanine-N7)-methylation / rRNA (guanine) methyltransferase activity / 90S preribosome / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / methyltransferase activity / small-subunit processome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / methylation / cytoplasmic translation / non-specific serine/threonine protein kinase / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Rio1 / : / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / Methyltransferase type 11 ...Serine/threonine-protein kinase Rio1 / : / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal / 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23-like / Methyltransferase involved in Williams-Beuren syndrome / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / Methyltransferase type 11 / Methyltransferase domain / : / RIO domain / Small-subunit processome, Utp14 / Utp14 protein / : / : / Eukaryotic type KH-domain (KH-domain type I) / K Homology domain, type 1 superfamily / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S7e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S8e / Ribosomal protein S27 / Ribosomal protein S24e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / K Homology domain / K homology RNA-binding domain / Tyrosine protein kinases specific active-site signature. / : / Tyrosine-protein kinase, active site / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15
Similarity search - Domain/homology
40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / 40S ribosomal protein S13-like protein / 40S ribosomal protein s9-like protein / 40S ribosomal protein S4 / Ribosomal protein s27-like protein / Serine/threonine-protein kinase RIO1 / Pre-rRNA-processing protein PNO1 / Small ribosomal subunit protein eS1 ...40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / 40S ribosomal protein S13-like protein / 40S ribosomal protein s9-like protein / 40S ribosomal protein S4 / Ribosomal protein s27-like protein / Serine/threonine-protein kinase RIO1 / Pre-rRNA-processing protein PNO1 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S7 / Uncharacterized protein / Methyltransferase-like protein / 40S ribosomal protein S11-like protein / 40S ribosomal protein S14-like protein / 40S ribosomal protein S22-like protein / Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLau B / Li Y / Zhu J / Fischer P / Hong X / Yuan R / Beckmann R / Hurt E / Cheng J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2026
Title: Nucleoplasmic checkpoint of the 40S ribosomal decoding center maturation.
Authors: Benjamin Lau / Yi Li / Jingyi Zhu / Xianwen Ye / Paulina Fischer / Xiaying Hong / Rui Yuan / Roland Beckmann / Ed Hurt / Jingdong Cheng /
Abstract: The decoding center (DC) is a key ribosomal structure for accurate translation, assembled in a multi-step process that starts on nucleolar pre-ribosomes and ends in the cytoplasm. While late ...The decoding center (DC) is a key ribosomal structure for accurate translation, assembled in a multi-step process that starts on nucleolar pre-ribosomes and ends in the cytoplasm. While late cytoplasmic steps and their checkpoint mechanisms are well characterized, the regulation of early nucleoplasmic DC assembly is unclear. Here, we show that the essential assembly factor Rrp12 plays a central coordinating role. Using Chaetomium thermophilum and cryo-electron microscopy analyses of fifteen pre-40S intermediates, we demonstrate that Rrp12 C terminus truncation: (1) inhibits release of the Utp14-Dhr1 pair, (2) displaces Tsr1, (3) promotes premature stabilization of h28, and (4) prevents h44 formation. These defects impair final 18S rRNA processing and prematurely activate the quality control kinase Rio1. Our results reveal a nucleoplasmic checkpoint during DC formation and establish Rrp12 as a critical regulator ensuring accurate assembly and orderly ribosome maturation.
History
DepositionOct 22, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66688.png

Downloads & links

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Map

FileDownload / File: emd_66688.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution filtered using Relion
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å		1.05 Å/pix.
x 360 pix.
= 376.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.1464946 - 0.26779023
Average (Standard dev.)-0.000059567737 (±0.005752972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 376.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: consensus refined map without postprocessing

Fileemd_66688_additional_1.map
Annotationconsensus refined map without postprocessing
Projections & Slices
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Additional map: local resolution filtered using deepEMhancer

Fileemd_66688_additional_2.map
Annotationlocal resolution filtered using deepEMhancer
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Half map: half map1

Fileemd_66688_half_map_1.map
Annotationhalf map1
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Half map: half map2

Fileemd_66688_half_map_2.map
Annotationhalf map2
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Sample components

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Entire : pre-40S ribosome, state Tsr1-1*

EntireName: pre-40S ribosome, state Tsr1-1*
Components
  • Complex: pre-40S ribosome, state Tsr1-1*
    • Protein or peptide: Small ribosomal subunit protein eS1
    • Protein or peptide: 40S ribosomal protein S4
    • Protein or peptide: 40S ribosomal protein S6
    • Protein or peptide: 40S ribosomal protein S7
    • Protein or peptide: 40S ribosomal protein S8
    • Protein or peptide: 40S ribosomal protein s9-like protein
    • Protein or peptide: 40S ribosomal protein S11-like protein
    • Protein or peptide: 40S ribosomal protein S13-like protein
    • Protein or peptide: 40S ribosomal protein S14-like protein
    • Protein or peptide: 40S ribosomal protein S22-like protein
    • Protein or peptide: 40S ribosomal protein s23-like protein
    • Protein or peptide: Small ribosomal subunit protein eS24
    • Protein or peptide: Ribosomal protein s27-like protein
    • Protein or peptide: 40S ribosomal protein S30
    • RNA: pre-18S
    • Protein or peptide: Methyltransferase-like protein
    • Protein or peptide: Pre-rRNA-processing protein PNO1
    • Protein or peptide: Serine/threonine-protein kinase RIO1
    • Protein or peptide: Utp14
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: pre-40S ribosome, state Tsr1-1*

SupramoleculeName: pre-40S ribosome, state Tsr1-1* / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: Small ribosomal subunit protein eS1

MacromoleculeName: Small ribosomal subunit protein eS1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 29.245158 KDa
SequenceString: MAVGKNKRLS KGKKGLKKKV QDPFTRKDWY NIKAPAPFAV RDVGKTLVNR TTGLKNANDA LKGRIFEVCL ADLQKDEDHA FRKIKLRVD EVQGKNCLTN FHGLDFTTDK LRSLVRKWQT LIEANVTVTT TDHYLLRLFA IAFTKRRPNQ IKKTTYAQSS Q IRAIRRKM ...String:
MAVGKNKRLS KGKKGLKKKV QDPFTRKDWY NIKAPAPFAV RDVGKTLVNR TTGLKNANDA LKGRIFEVCL ADLQKDEDHA FRKIKLRVD EVQGKNCLTN FHGLDFTTDK LRSLVRKWQT LIEANVTVTT TDHYLLRLFA IAFTKRRPNQ IKKTTYAQSS Q IRAIRRKM VEIIQREAAS CTLHQLVSKL IPEVIGREIE KATQGIYPLQ NVHIRKVKLL KQPKFDLGAL MALHGESSEE AG QKVEREF REQVLESV

UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #2: 40S ribosomal protein S4

MacromoleculeName: 40S ribosomal protein S4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 29.800764 KDa
SequenceString: MARGPKKHQK RLSAPSHWLL DKLSGAYAPR PSTGPHKLRD CMPLIVFVRN RLKYALNYRE TKAIMMQRLV KVDGKVRTDI TYPAGFMDV ITIEKTGENF RLIYDTKGRF TVHRITDEEA KYKLGKVKRV QLGRGGVPFL VTHDARTIRY PDPLIKVNDT V KIDLETGK ...String:
MARGPKKHQK RLSAPSHWLL DKLSGAYAPR PSTGPHKLRD CMPLIVFVRN RLKYALNYRE TKAIMMQRLV KVDGKVRTDI TYPAGFMDV ITIEKTGENF RLIYDTKGRF TVHRITDEEA KYKLGKVKRV QLGRGGVPFL VTHDARTIRY PDPLIKVNDT V KIDLETGK ITDFIKFDTG ALAMITGGRN MGRVGVITHR ERHDGGFGIV HLKDALDNTF ATRESNVFVI GSEKPWISLP KG KGVKLTI AEERDQRRAR ALAAAGH

UniProtKB: 40S ribosomal protein S4

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Macromolecule #3: 40S ribosomal protein S6

MacromoleculeName: 40S ribosomal protein S6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 27.490139 KDa
SequenceString: MKLNISHPAN GSQKLIEVED ERKLRHFYDK RMGAEVAGDP LGPEWKGYIL RITGGNDKQG FPMKQGVIAP NRVRLLLSEG HSCYRPRRD GERKRKSVRG CIVGPDLSVL ALSIVKQGEQ DIPGLTDVVH PKRLGPKRAT KIRRFFSLSK DDDVRKYVIR R EVQPKGEG ...String:
MKLNISHPAN GSQKLIEVED ERKLRHFYDK RMGAEVAGDP LGPEWKGYIL RITGGNDKQG FPMKQGVIAP NRVRLLLSEG HSCYRPRRD GERKRKSVRG CIVGPDLSVL ALSIVKQGEQ DIPGLTDVVH PKRLGPKRAT KIRRFFSLSK DDDVRKYVIR R EVQPKGEG KKPYTKAPRI QRLVTPQRLQ HKRHRIALKR RQQEKVKEEA AEYAQILAKR VAEAKAQKAD LRKRRASSLH K

UniProtKB: 40S ribosomal protein S6

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Macromolecule #4: 40S ribosomal protein S7

MacromoleculeName: 40S ribosomal protein S7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 23.08465 KDa
SequenceString: MSAPSLNKIA ANSPSRQNPS DLERAIAGAL YDLETNTADL KAALRPLQFV SAREIEVGHG KKAIVIFVPV PALQGFHRVQ QRLTRELEK KFSDRHVLIL AARRILPKPK RSARSRNTLK QKRPRSRTLT AVHDAILTDL VYPVEIVGKR LRTKEDGSKV L KVILDEKE ...String:
MSAPSLNKIA ANSPSRQNPS DLERAIAGAL YDLETNTADL KAALRPLQFV SAREIEVGHG KKAIVIFVPV PALQGFHRVQ QRLTRELEK KFSDRHVLIL AARRILPKPK RSARSRNTLK QKRPRSRTLT AVHDAILTDL VYPVEIVGKR LRTKEDGSKV L KVILDEKE RGGVDYRLDT YSEVYRRLTG RNVTFEFPQT TITDY

UniProtKB: 40S ribosomal protein S7

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Macromolecule #5: 40S ribosomal protein S8

MacromoleculeName: 40S ribosomal protein S8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 23.102416 KDa
SequenceString: MGISRDSRHK RSHTGAKRAF YRKKRAFELG RQPANTRIGP KRIHIVRTRG GNHKYRALRL DSGNFAWGSE GCTRKTRIIG VVYHPSNNE LVRTNTLTKS AVVQIDAAPF RQWYEAHYGQ PLGRRRQQKQ GQVVEEVKKS KSVEKKQAAR FAAHGKVDPA L EKQFEAGR ...String:
MGISRDSRHK RSHTGAKRAF YRKKRAFELG RQPANTRIGP KRIHIVRTRG GNHKYRALRL DSGNFAWGSE GCTRKTRIIG VVYHPSNNE LVRTNTLTKS AVVQIDAAPF RQWYEAHYGQ PLGRRRQQKQ GQVVEEVKKS KSVEKKQAAR FAAHGKVDPA L EKQFEAGR LYAIISSRPG QSGRADGYIL EGEELAFYQR KLHK

UniProtKB: 40S ribosomal protein S8

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Macromolecule #6: 40S ribosomal protein s9-like protein

MacromoleculeName: 40S ribosomal protein s9-like protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 22.029836 KDa
SequenceString:
MAPRKYSKTY KVPRRPYEAA RLDSELKLVG EYGLRNKREV WRVLLTLSKI RRAARILLTL DEKDPKRLFE GNALIRRLVR IGVLDESRM KLDYVLALKA EDFLERRLQT LVYKLGLAKS IHHARVLIRQ RHIRVGKQIV NVPSFMVRLD SQKHIDFALT S PFGGGRPG RVRRKKAKAA EGGEGGEEEE EE

UniProtKB: 40S ribosomal protein s9-like protein

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Macromolecule #7: 40S ribosomal protein S11-like protein

MacromoleculeName: 40S ribosomal protein S11-like protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 18.698182 KDa
SequenceString:
MATELTVQSE RAFLKQPHIF LNSKVKVKST RPGKGGRRWY KDVGLGFKTP KTAIEGHYID KKCPFTGMVS IRGRILTGRV VSTKMHRTI IIRREYLHYI PKYNRYEKRH KNLAAHVSPA FRVEEGDMVV VGQCRPLSKT VRFNVLRVLP RTGKSVKKFQ K F

UniProtKB: 40S ribosomal protein S11-like protein

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Macromolecule #8: 40S ribosomal protein S13-like protein

MacromoleculeName: 40S ribosomal protein S13-like protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 16.912891 KDa
SequenceString:
MGRLHSKGKG ISASAIPYSR NPPAWLKTTP EQVVEQICKL ARKGATPSQI GVILRDSHGI AQVKVVTGNK ILRILKSNGL APDIPEDLY FLIKKAVAVR KHLERNRKDK DSKFRLILIE SRIHRLARYY KTVGVLPPTW KYESSTASTL VA

UniProtKB: 40S ribosomal protein S13-like protein

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Macromolecule #9: 40S ribosomal protein S14-like protein

MacromoleculeName: 40S ribosomal protein S14-like protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 16.071464 KDa
SequenceString:
MPPKKTTRPA QENISLGPQV REGELVFGVA RIFASFNDTF VHVTDLSGRE TICRVTGGMK VKADRDESSP YAAMLAAQDV AARCKELGI TALHIKIRAT GGNGTKTPGP GAQSALRALA RSGMKIGRIE DVTPTPSDST RRKGGRRGRR L

UniProtKB: 40S ribosomal protein S14-like protein

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Macromolecule #10: 40S ribosomal protein S22-like protein

MacromoleculeName: 40S ribosomal protein S22-like protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 14.905471 KDa
SequenceString:
MVRTSVLHDA LNSINNAEKM GKRQVMIRPS SKVIVKFLQV MQRHGYIGEF EEVDNHRSGK IVVQLNGRLN KCGVISPRYN VRLAELEKW VTKLLPARQF GYVILTTSAG IMDHEEARRK HVAGKIIGFF Y

UniProtKB: 40S ribosomal protein S22-like protein

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Macromolecule #11: 40S ribosomal protein s23-like protein

MacromoleculeName: 40S ribosomal protein s23-like protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 15.934653 KDa
SequenceString:
MSGGKPRGLN AARKLRNNRR EQRWADLQYK KRALGTAYKS SPFGGSSHAK GIVLEKVGVE AKQPNSAIRK CVRVQLIKNG KKVTAFVPN DGCLNFVDEN DEVLLAGFGR KGKAKGDIPG VRFKVVKVSG VGLLALWKEK KEKPRS

UniProtKB: 40S ribosomal protein s23-like protein

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Macromolecule #12: Small ribosomal subunit protein eS24

MacromoleculeName: Small ribosomal subunit protein eS24 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 15.535286 KDa
SequenceString:
MADTDSPVTL RTRKFIRNPL LSRKQMVVDI LHPGRPNISK DELREKLATM YKAQKDQVSV FGLRTQYGGG KTTGFALIYD SPEALKKFE PRYRLVRAGL AAKVEKASRQ QRKQRKNRLK TLRGTAKVKG AKAKKEK

UniProtKB: Small ribosomal subunit protein eS24

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Macromolecule #13: Ribosomal protein s27-like protein

MacromoleculeName: Ribosomal protein s27-like protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 8.923572 KDa
SequenceString:
MVLAVDLLNP SPASEARKHK LKTLVPAPRS FFMDVKCPGC FTITTVFSHA QTVVICQGCT NVLCQPTGGK ARLTEGCSFR RK

UniProtKB: Ribosomal protein s27-like protein

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Macromolecule #14: 40S ribosomal protein S30

MacromoleculeName: 40S ribosomal protein S30 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 6.917273 KDa
SequenceString:
MGKVHGSLAR AGKVKSQTPK VEKQEKPKTP KGRAKKRLLY TRRFVNITVV GGKRKMNPNP GN

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Macromolecule #16: Methyltransferase-like protein

MacromoleculeName: Methyltransferase-like protein / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 30.362834 KDa
SequenceString: MSRPEDTLAA DVHYNDAEAR KYTTSSRIQN IQAAMTRRAL ELLNLKSPSL ILDVGCGSGL SGEILSSVPP EEGGPHVWVG MDISASMLD VALQRDVEGD LLLSDIGQGV PFRPGTFDAA ISISAIQWLC NADTSETSPA GRLTRFFNGL YAALKRGGMA V CQFYPKND ...String:
MSRPEDTLAA DVHYNDAEAR KYTTSSRIQN IQAAMTRRAL ELLNLKSPSL ILDVGCGSGL SGEILSSVPP EEGGPHVWVG MDISASMLD VALQRDVEGD LLLSDIGQGV PFRPGTFDAA ISISAIQWLC NADTSETSPA GRLTRFFNGL YAALKRGGMA V CQFYPKND VQKQMITSAA IKAGFGAGLL EDDPGTKNVK VYLVLTVGST AVQAKGGDIT GVVEGMDNVE VLDNRKKAKP KS GKGEIKK GSKAWIIKKK EQMERKGKIV KRTSKYTGRS RGPKF

UniProtKB: Methyltransferase-like protein

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Macromolecule #17: Pre-rRNA-processing protein PNO1

MacromoleculeName: Pre-rRNA-processing protein PNO1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 28.715047 KDa
SequenceString: MPAPTALKQP PPAPEQQAAP AITNENEDEL LIDIQQAAAT LTDPNAAEPP EETMENEMAV DEEGRPRFAP GKNIDPIRRI ETRKIPIPP HRMSALKANW TKYPPLVDHC KLQVRMNIKE KRVELRSSKY TVSNEALQMG ADFVSAFAMG FDIDDAIALL R LDSLYIQS ...String:
MPAPTALKQP PPAPEQQAAP AITNENEDEL LIDIQQAAAT LTDPNAAEPP EETMENEMAV DEEGRPRFAP GKNIDPIRRI ETRKIPIPP HRMSALKANW TKYPPLVDHC KLQVRMNIKE KRVELRSSKY TVSNEALQMG ADFVSAFAMG FDIDDAIALL R LDSLYIQS FDIKDVRQTL GPDALSRAIG RIAGKDGKTK FAIENATKTR IVLAGSKVHI LGAFENIGMA RESIVSLVLG AQ PGKVYNN LRIIASRMKE RW

UniProtKB: Pre-rRNA-processing protein PNO1

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Macromolecule #18: Serine/threonine-protein kinase RIO1

MacromoleculeName: Serine/threonine-protein kinase RIO1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 59.374414 KDa
SequenceString: MTPAPEPQDP PTIHEPVATE QTDDISDWDV ESDYEDGYGA PSKSQAQGGA SAADRPKINA HARIDDQMTD LARHASKIRL DNLTMQQIF RDKDRTDNAT SDQVLDNHTR MIILNMLNRN IISEIYGTIS TGKEANVYNA VAYDNNGERI ERAVKVYKTI I LGFKDRER ...String:
MTPAPEPQDP PTIHEPVATE QTDDISDWDV ESDYEDGYGA PSKSQAQGGA SAADRPKINA HARIDDQMTD LARHASKIRL DNLTMQQIF RDKDRTDNAT SDQVLDNHTR MIILNMLNRN IISEIYGTIS TGKEANVYNA VAYDNNGERI ERAVKVYKTI I LGFKDRER YLAGEQRFKT IVDKALSAPR KMIKLWAEKE FRNLKRLHTA GIPCPEPIYL KYNVMVMGFL GDHTNGYAFP RL HDTKITG ETLEETEAEW RRLYINLLSM MRRMYQVCGL VHGDLSEYNI LYNEGVLYII DVSQSVEHDH IEATNFLRMD IRN VNDFFA RRGVDTLSDR TVYHFITDST GAVDENGMRK AIDNLYATRP PLAESEEARA EQEIDNQVFR NQFIPTTLEE VYNL EVELG KKVDTRLYQH MLADSKVPES TGGEHKSGEG GESGSEDEEG DEGESGEVES GDEEREEGEG DRFEKKRPRG KKHLD KAEK HAHKMAVKEA KREKRKEKMP KHVKKKLVAA NKKRK

UniProtKB: Serine/threonine-protein kinase RIO1

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Macromolecule #19: Utp14

MacromoleculeName: Utp14 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 104.741391 KDa
SequenceString: MPGRQAHGRP LLPSLGSSSG GGKSKKSRSK ARRSAQSKAL DAFALAAEQV PESRSKGVRL RDLDEHPSTS ASRNKRQHED DEEDDFDGF DDDEGMGRKK RARRDSGGDE DGDDVDEDME GGADGEDDSE EWHVGVTGAD EDSEIDSDEA FGESDEERFE G FVFGGSKS ...String:
MPGRQAHGRP LLPSLGSSSG GGKSKKSRSK ARRSAQSKAL DAFALAAEQV PESRSKGVRL RDLDEHPSTS ASRNKRQHED DEEDDFDGF DDDEGMGRKK RARRDSGGDE DGDDVDEDME GGADGEDDSE EWHVGVTGAD EDSEIDSDEA FGESDEERFE G FVFGGSKS HKKGTKKRRN GSEDDAIDLA TALDQYESSE EGEEGEESES EEDDEESEEE DSDEEDDDPS KLDALQSMIA GF AGEDEES GGEGEAKPSG KQKLSLKDLG LVGVKDPDMK RSLRLMKKEE KATKPGSSKK LEVPLAKRQQ DRLMREAAYK KTN ETLDRW IETVKHNRRA EHLVFPLAQN AHDRGLDASE LQPITQKTSG TELEQTILAI MEESGLGPTA KPEKKETSGE AGKQ GMSKE EQKELIRQKR RERELHSREM ARLKRIKKIK SKTWRRIHRK ELLKNEEAAY QAALEAGELD SEEEREALDR RRALE RVGA RHKESKWAKL GKKAGRAVWD EDFRAGLAEM ARRKDELRKR IEGLKNGSDD SSDDSDGDED ASGDEAAERR KLLAEL EKA AAYSDDDEPH SKLFQLKFMQ RGEELRRKEN EELIAQIRRE LDSDYDGSEP DEVEIGRRTF GMGKKDKTEQ QQAQDQL AR MQAAEARKEK AAARVAAAEE TVKQEAREKA EKDEASAPST AGAWSQPKVE AGAWSKPDDE GSSKPRKAPK GRPEEIDV T DLALAGKPAK AKANGQAKSQ VQGKAHASNG QSSSSQKAST SVAITGAEED GNDSDDSDAV HLPMAIRDRA LIERAFAGD DVAAEFEKEK AEIEADDDEK EIDNTLPGWG SWVGEGVSNR EKRRHQGRFV TKVEGIKKEK RKDYKLKDVI INEKRVKKND KYLATGLPH PFESQQQYER SLRLPVGPEW MTKETFQDAT KPRVIIKQGI IAPMSKPMY

UniProtKB: Uncharacterized protein

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Macromolecule #15: pre-18S

MacromoleculeName: pre-18S / type: rna / ID: 15 / Number of copies: 1
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 579.124812 KDa
SequenceString: UACCUGGUUG AUUCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUAUACAG CGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUAC CUUACUACAU GGAUAACCGU GGUAAUUCUA G AGCUAAUA ...String:
UACCUGGUUG AUUCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUAUACAG CGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUAC CUUACUACAU GGAUAACCGU GGUAAUUCUA G AGCUAAUA CAUGCUGAAA AUCCCGACUU CGGAAGGGAU GUAUUUAUUA GAUUAAAAAC CAAUGCCCUU CGGGGCUUUC UG GUGAUUC AUAAUAACUU CUCGAAUCGC ACGGCCUUGC GCCGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGA CGGCUG GGUAUUGGCC AGCCGUGGUG ACAACGGGUA ACGGAGGGUU AGGGCUCGAC CCCGGAGAAG GAGCCUGAGA AACG GCUAC UACAUCCAAG GAAGGCAGCA GGCGCGCAAA UUACCCAAUC CCGACACGGG GAGGUAGUGA CAAUAAAUAC UGAUA CAGG GCUCUUUCGG GUCUUGUAAU UGGAAUGAGU ACAAUUUAAA UCCCUUAACG AGGAACAAUU GGAGGGCAAG UCUGGU GCC AGCAGCCGCG GUAAUUCCAG CUCCAAUAGC GUAUAUUAAA GUUGUUGAGG UUAAAAAGCU CGUAGUUGAA CCUUGGG CC UAGCCCGCCG GUCCGCCUCA CCGCGUGCAC UGGCUGGGCU GGGCCUUUCC UUCUGGAGAA CCGCAUGCCC UUCACUGG G UGUGUCGGGG AACCAGGACU UUUACUCUGA ACAAAUUAGA UCGCUUAAAG AAGGCCUAUG CUUGAAUACA UUAGCAUGG AAUAAUAGAA UAGGACGUGU GGUUCUAUUU UGUUGGUUUC UAGGACCGCC GUAAUGAUUA AUAGGGACAG UCGGGGGCGU CAGUAUUCA AUUGUCAGAG GUGAAAUUCU UGGAUUUAUU GAAGACUAAC AACUGCGAAA GCAUUCGCCA AGGAUGUUUU C AUUAAUCA GGAACGAAAG UUAGGGGAUC GAAGACGAUC AGAUACCGUC GUAGUCUUAA CCAUAAACUA UGCCGAUUAG GG AUCGGAC GGCGUUUAUU UUUGACCCGU UCGGCACCUU ACGAUAAAUC AAAAUGUUUG GGCUCCUGGG GGAGUAUGGU CGC AAGGCU GAAACUUAAA GAAAUUGACG GAAGGGCACC ACCAGGGGUG GAGCCUGCGG CUUAAUUUGA CUCAACACGG GGAA ACUCA CCAGGUCCAG ACACGAUGAG GAUUGACAGA UUGAGAGCUC UUUCUUGAUU UCGUGGGUGG UGGUGCAUGG CCGUU CUUA GUUGGUGGAG UGAUUUGUCU GCUUAAUUGC GAUAACGAAC GAGACCUUAA CCUGCUAAAU AGCCCGUAUU GCCUUG GCA GUACGCCGGC UUCUUAGAGG GACUAUCGGC UCAAGCCGAU GGAAGUUUGA GGCAAUAACA GGUCUGUGAU GCCCUUA GA UGUUCUGGGC CGCACGCGCG CUACACUGAC AGAGCCAGCG AGUACUCCCU UGGCCGAGAG GCCCGGGUAA UCUUGUUA A ACUCUGUCGU GCUGGGGAUA GAGCAUUGCA AUUAUUGCUC UUCAACGAGG AAUCCCUAGU AAGCGCAAGU CAUCAGCUU GCGUUGAUUA CGUCCCUGCC CUUUGUACAC ACCGCCCGUC GCUACUACCG AUUGAACGGC UCAGUGAGGC UUUCGGACUG GCCCAGAGA GGUCGGCAAC GACCACUCAG GGCCGGAAAG UUAUCCAAAC UCGGUCGUUU AGAGGAAGUA AAAGUCGUAA C AAGGUCUC CGUAGGUGAA CCUGCGGAGG GAUCAUUAA

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Macromolecule #20: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Details: Relion / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6g18

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 6707
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
Final angle assignmentType: OTHER / Software - Name: RELION / Details: Relion
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6g18


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9xai:
Cryo-EM structure of the pre-40S ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum, state Tsr1-1*

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