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- PDB-9yfm: insect H/ACA snoRNP class II composite -

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Basic information

Entry
Database: PDB / ID: 9yfm
Titleinsect H/ACA snoRNP class II composite
Components
  • H/ACA ribonucleoprotein complex subunit
  • H/ACA ribonucleoprotein complex subunit 2-like protein
  • H/ACA ribonucleoprotein complex subunit 3
  • H/ACA ribonucleoprotein complex subunit 4-like
  • RNA (96-MER)
KeywordsRNA BINDING PROTEIN / Pseudouridine synthase / enzyme complex / snoRNA / snoRNP
Function / homology
Function and homology information


snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis / box H/ACA snoRNA binding / pseudouridine synthase activity / positive regulation of telomerase RNA localization to Cajal body / telomerase RNA binding ...snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis / box H/ACA snoRNA binding / pseudouridine synthase activity / positive regulation of telomerase RNA localization to Cajal body / telomerase RNA binding / snoRNA binding / ribonucleoprotein complex / RNA binding
Similarity search - Function
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 ...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 / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / PUA domain profile. / PUA-like superfamily / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / H/ACA ribonucleoprotein complex subunit 4-like / H/ACA ribonucleoprotein complex subunit 3 / H/ACA ribonucleoprotein complex subunit 2-like protein / H/ACA ribonucleoprotein complex subunit
Similarity search - Component
Biological speciesTrichoplusia ni (cabbage looper)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsPanwar, H.S. / Worden, E.W.
Funding support United States, Canada, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM147261-01 United States
Canadian Institutes of Health Research (CIHR)437623 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Interprotomer communication and functional asymmetry in H/ACA snoRNPs.
Authors: Hemendra Singh Panwar / Timothy J Vos / Xiaoyan Xie / H Josh Jang / Hyoungjoo Lee / Ryan D Sheldon / Evan J Worden / Ute Kothe /
Abstract: H/ACA small nucleolar ribonucleoproteins (H/ACA snoRNPs) facilitate essential cellular processes such as RNA modification, folding, and stability. Here, we present multiple cryo-EM structures of ...H/ACA small nucleolar ribonucleoproteins (H/ACA snoRNPs) facilitate essential cellular processes such as RNA modification, folding, and stability. Here, we present multiple cryo-EM structures of endogenous insect H/ACA snoRNPs containing two protomers assembled on a two-hairpin H/ACA snoRNA. By characterizing key protein-protein and protein-RNA interactions, we reveal the coordination of pseudouridylation activity across the two protomers which explains the predominance of two-hairpin structures in eukaryotic H/ACA snoRNAs. Moreover, we found that several mutations in H/ACA proteins associated with dyskeratosis congenita (DC) directly impair pseudouridine formation suggesting how these mutations disrupt RNA modification and ribosome biogenesis in this disease. Additionally, we uncover coordinated structural changes between Nop10, Nhp2, and the N-terminal extensions of Cbf5 in the 3' protomer that resemble active and inactive conformations and may regulate H/ACA snoRNP activity. In summary, this study provides detailed insight into the structure and function of RNA modification-competent H/ACA snoRNPs, which play pivotal roles in cellular processes including ribosome biogenesis, rRNA folding, (m)RNA modification, and telomere maintenance.
History
DepositionSep 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Revision 1.2Dec 31, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: H/ACA ribonucleoprotein complex subunit
C: H/ACA ribonucleoprotein complex subunit 2-like protein
E: H/ACA ribonucleoprotein complex subunit
F: H/ACA ribonucleoprotein complex subunit 3
G: H/ACA ribonucleoprotein complex subunit 2-like protein
H: H/ACA ribonucleoprotein complex subunit 3
A: H/ACA ribonucleoprotein complex subunit 4-like
D: H/ACA ribonucleoprotein complex subunit 4-like
I: RNA (96-MER)


Theoretical massNumber of molelcules
Total (without water)242,4409
Polymers242,4409
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein H/ACA ribonucleoprotein complex subunit


Mass: 22800.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) / References: UniProt: A0A7E5WAP8
#2: Protein H/ACA ribonucleoprotein complex subunit 2-like protein


Mass: 17704.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) / References: UniProt: A0A7E5W3Q7
#3: Protein H/ACA ribonucleoprotein complex subunit 3 / Nucleolar protein 10 / Nucleolar protein family A member 3 / snoRNP protein NOP10


Mass: 7607.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) / References: UniProt: A0A7E5W2Q0
#4: Protein H/ACA ribonucleoprotein complex subunit 4-like


Mass: 57643.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) / References: UniProt: A0A7E5VBG0
#5: RNA chain RNA (96-MER)


Mass: 30928.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Insect H/ACA snoRNP / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 733250 / Symmetry type: POINT
RefinementCross valid method: NONE

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