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- EMDB-72902: insect H/ACA snoRNP class III -

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Basic information

Entry
Database: EMDB / ID: EMD-72902
Titleinsect H/ACA snoRNP class III
Map dataMain volume data
Sample
  • Complex: Insect H/ACA snoRNP
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 4-like
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 3
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 2-like protein
    • RNA: RNA (76-MER)
KeywordsPseudouridine synthase / enzyme complex / snoRNA / snoRNP / RNA BINDING PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsPanwar HS / Worden EW
Funding support United States, Canada, 2 items
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, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72902.png

Downloads & links

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Map

FileDownload / File: emd_72902.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain volume data
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.4 Å		0.83 Å/pix.
x 300 pix.
= 248.4 Å		0.83 Å/pix.
x 300 pix.
= 248.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0652
Minimum - Maximum-0.0018024003 - 2.7385623
Average (Standard dev.)0.0014856362 (±0.0281876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional volume data

Fileemd_72902_additional_1.map
AnnotationAdditional volume data
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half volume data

Fileemd_72902_half_map_1.map
Annotationhalf volume data
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half volume data

Fileemd_72902_half_map_2.map
Annotationhalf volume data
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Insect H/ACA snoRNP

EntireName: Insect H/ACA snoRNP
Components
  • Complex: Insect H/ACA snoRNP
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 4-like
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 3
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 2-like protein
    • RNA: RNA (76-MER)

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Supramolecule #1: Insect H/ACA snoRNP

SupramoleculeName: Insect H/ACA snoRNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: H/ACA ribonucleoprotein complex subunit 4-like

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 4-like / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 57.643172 KDa
SequenceString: MTEVLQPGAE VFSEKKKKKV KESKEGVSLG QFQKLGDFKI EPTESVTKLD TAYWPLLLKN FDRLNVRTNH YTPLPFGHSP LKRPIAEYV KAGFINVDKP SNPSSHEVVS WIKRILKVEK TGHSGTLDPK VTGCLIVCID RATRLVKSQQ NAGKEYVAVF S LHSAVENV ...String:
MTEVLQPGAE VFSEKKKKKV KESKEGVSLG QFQKLGDFKI EPTESVTKLD TAYWPLLLKN FDRLNVRTNH YTPLPFGHSP LKRPIAEYV KAGFINVDKP SNPSSHEVVS WIKRILKVEK TGHSGTLDPK VTGCLIVCID RATRLVKSQQ NAGKEYVAVF S LHSAVENV KKVTQGLEKL RGALFQRPPL ISAVKRQLRV RSVYDSKLLD FDKDRNIGVF WVSCEAGSYI RTMCVHLGLM LG VGGQMIE LRRVRSGIQG EKEGMVTMHD ILDAQWAYEN HKDESYLRRV IKPLEGLLVA HKRIFIKDSA VNAVCYGAKV LLP GILRYE DGIEIDQEIV IVTTKGEAVA LAIALMTTST MASCDHGVAA KLKRVIMERD TYPRKWGLGP KASHKKSLIS QGKL DKFGK PNENTPSEWL NSYVDYKKKD TNGDAEDDVG RKRTASTANA DDPDNSVEVK SEKKKKKKKR DSEAADAVPE DGSGD ATME AETTTEADSS IRKEKKKKKK KDREQERVDE

UniProtKB: H/ACA ribonucleoprotein complex subunit 4-like

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Macromolecule #2: H/ACA ribonucleoprotein complex subunit

MacromoleculeName: H/ACA ribonucleoprotein complex subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 22.800066 KDa
SequenceString: MSFRGRGGGG GGRGGYGGGG GGGGRGFGGR GGGGGRGGFG GRGGGRGGRG GGGGGFRQQD QGPPESVIPL GHYGWTVQDD LICKVDIED VPYFNAPIFL ENKEQIGKID EIFGNLRDYF VSVKMGDNFK ANSFKDGQQF YIDPAKLLPL KRFLPQPPGA K RGGGRGRG ...String:
MSFRGRGGGG GGRGGYGGGG GGGGRGFGGR GGGGGRGGFG GRGGGRGGRG GGGGGFRQQD QGPPESVIPL GHYGWTVQDD LICKVDIED VPYFNAPIFL ENKEQIGKID EIFGNLRDYF VSVKMGDNFK ANSFKDGQQF YIDPAKLLPL KRFLPQPPGA K RGGGRGRG GPRGGRGGGG GFGRGGGGGG RGGGFGRGGG GGRGGFGRGG GGGYGGGGGG FNRGGGGFRG GRGGR

UniProtKB: H/ACA ribonucleoprotein complex subunit

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Macromolecule #3: H/ACA ribonucleoprotein complex subunit 3

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 7.607749 KDa
SequenceString:
MYLRYYLNEN GDRQYTLATI DPYGKPTISA HPARFSPEDK YSRHRIIIKK RFGLLLTQQP EPIL

UniProtKB: H/ACA ribonucleoprotein complex subunit 3

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Macromolecule #4: H/ACA ribonucleoprotein complex subunit 2-like protein

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 2-like protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 17.704756 KDa
SequenceString:
MGKIKQEPVE QEDQADVSVK NEPQSYDEKV DHCSVIAKPM APKKLSKKIY KLIKKSTSHK NYIRNGLKIV QKQLRLGEKG IVFFAGDIS PIEIMCHLPA VCEEKDIPYC YTPSRKDIGA AMGTMRGCVM VLVKEHDDYK DLFDEVRGEI KLLGHPI

UniProtKB: H/ACA ribonucleoprotein complex subunit 2-like protein

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Macromolecule #5: RNA (76-MER)

MacromoleculeName: RNA (76-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 24.486674 KDa
SequenceString:
CCUGCGGCGU GCACGUCCCA ACUGGGACGU GCACCGGCCG CAGGAACAGC AACGGAGCGA GUACUCGCUC ACACAU

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134862
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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