9YFL | pdb_00009yfl

insect H/ACA snoRNP class I

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2025-09-26 Released: 2025-12-10 
  • Deposition Author(s): Panwar, H.S., Worden, E.W.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interprotomer communication and functional asymmetry in H/ACA snoRNPs.

Panwar, H.S.Vos, T.J.Xie, X.Jang, H.J.Lee, H.Sheldon, R.D.Worden, E.J.Kothe, U.

(2025) Proc Natl Acad Sci U S A 122: e2514683122-e2514683122

  • DOI: https://doi.org/10.1073/pnas.2514683122
  • Primary Citation of Related Structures:  
    9YFL, 9YFM, 9YFN, 9YFO

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 3A [auth F],
F [auth H]
64Trichoplusia niMutation(s): 0 
UniProt
Find proteins for A0A7E5W2Q0 (Trichoplusia ni)
Explore A0A7E5W2Q0 
Go to UniProtKB:  A0A7E5W2Q0
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UniProt GroupA0A7E5W2Q0
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 4-likeB [auth A],
D
514Trichoplusia niMutation(s): 0 
UniProt
Find proteins for A0A7E5VBG0 (Trichoplusia ni)
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Go to UniProtKB:  A0A7E5VBG0
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UniProt GroupA0A7E5VBG0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunit 2-like proteinC,
E [auth G]
156Trichoplusia niMutation(s): 0 
UniProt
Find proteins for A0A7E5W3Q7 (Trichoplusia ni)
Explore A0A7E5W3Q7 
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UniProt GroupA0A7E5W3Q7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H/ACA ribonucleoprotein complex subunitG [auth B],
H [auth E]
233Trichoplusia niMutation(s): 0 
UniProt
Find proteins for A0A7E5WAP8 (Trichoplusia ni)
Explore A0A7E5WAP8 
Go to UniProtKB:  A0A7E5WAP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7E5WAP8
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
Modeled RNA (101-MER)137Trichoplusia ni
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM147261-01
Canadian Institutes of Health Research (CIHR)Canada437623

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-31
    Changes: Data collection, Database references