[English] 日本語
Yorodumi
- EMDB-72898: insect H/ACA snoRNP class II composite -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72898
Titleinsect H/ACA snoRNP class II composite
Map dataComposite Map for class II snoRNP
Sample
  • Complex: Insect H/ACA snoRNP
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 2-like protein
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 3
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 4-like
    • RNA: RNA (96-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: 2.95 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.USA / Year: 2025
Title: Interprotomer communication and functional asymmetry in H/ACA snoRNP
Authors: Panwar HS / Vos T / Xie X / Jang HS / Lee H / Sheldon RD / Worden EJ / Kothe U
History
DepositionSep 26, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72898.png

Downloads & links

-
Map

FileDownload / File: emd_72898.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite Map for class II snoRNP
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: 0.0421
Minimum - Maximum-0.001705707 - 2.3547719
Average (Standard dev.)0.0016697528 (±0.0262227)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
Entire : Insect H/ACA snoRNP

EntireName: Insect H/ACA snoRNP
Components
  • Complex: Insect H/ACA snoRNP
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 2-like protein
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 3
    • Protein or peptide: H/ACA ribonucleoprotein complex subunit 4-like
    • RNA: RNA (96-MER)

-
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)

-
Macromolecule #1: H/ACA ribonucleoprotein complex subunit

MacromoleculeName: H/ACA ribonucleoprotein complex subunit / type: protein_or_peptide / ID: 1 / 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

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

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 2-like protein
type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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

-
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

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

MacromoleculeName: H/ACA ribonucleoprotein complex subunit 4-like / type: protein_or_peptide / ID: 4 / 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

-
Macromolecule #5: RNA (96-MER)

MacromoleculeName: RNA (96-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 30.92852 KDa
SequenceString:
CCUGCGGCGU GCACGUCCCA ACUGGGACGU GCACCGGCCG CAGGAACAGC AACGGAGCGA UGCACGUCCC AACUGGGACG UGCACCGCU CACACAU

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 733250
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more