[English] 日本語
Yorodumi
- PDB-7bgb: The H/ACA RNP lobe of human telomerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bgb
TitleThe H/ACA RNP lobe of human telomerase
Components
  • (H/ACA ribonucleoprotein complex subunit ...) x 4
  • RNA (92-MER)
  • Telomerase Cajal body protein 1
KeywordsRNA BINDING PROTEIN / H/ACA RNP / ribonucleoprotein / complex / RNA
Function / homology
Function and homology information


telomere formation via telomerase / box H/ACA scaRNP complex / box H/ACA telomerase RNP complex / protein localization to Cajal body / snoRNA guided rRNA pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis ...telomere formation via telomerase / box H/ACA scaRNP complex / box H/ACA telomerase RNP complex / protein localization to Cajal body / snoRNA guided rRNA pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / Isomerases; Intramolecular transferases; Transferring other groups / Cajal body organization / telomerase RNA stabilization / snRNA pseudouridine synthesis / regulation of telomerase RNA localization to Cajal body / mRNA pseudouridine synthesis / box H/ACA snoRNA binding / pseudouridine synthase activity / protein carrier chaperone / telomerase RNA localization to Cajal body / telomerase activity / positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / RNA folding chaperone / sno(s)RNA-containing ribonucleoprotein complex / telomerase holoenzyme complex / telomerase RNA binding / U3 snoRNA binding / rRNA modification in the nucleus and cytosol / positive regulation of double-strand break repair via nonhomologous end joining / positive regulation of double-strand break repair / telomerase holoenzyme complex assembly / Association of TriC/CCT with target proteins during biosynthesis / Telomere Extension By Telomerase / RNA folding / telomere maintenance via telomerase / RNA processing / Cajal body / positive regulation of double-strand break repair via homologous recombination / positive regulation of telomere maintenance via telomerase / positive regulation of DNA repair / mRNA 3'-UTR binding / fibrillar center / rRNA processing / protein-folding chaperone binding / site of double-strand break / histone binding / chromosome, telomeric region / nuclear body / DNA repair / ubiquitin protein ligase binding / protein-containing complex binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 ...: / 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. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / 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 / WD domain, G-beta repeat / Translation protein, beta-barrel domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / H/ACA ribonucleoprotein complex subunit DKC1 / Telomerase Cajal body protein 1 / H/ACA ribonucleoprotein complex subunit 3 / H/ACA ribonucleoprotein complex subunit 2 / H/ACA ribonucleoprotein complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNguyen, T.H.D. / Ghanim, G.E. / Fountain, A.J. / van Roon, A.M.M. / Rangan, R. / Das, R. / Collins, K.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/19 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM054198 United States
CitationJournal: Nature / Year: 2021
Title: Structure of human telomerase holoenzyme with bound telomeric DNA.
Authors: George E Ghanim / Adam J Fountain / Anne-Marie M van Roon / Ramya Rangan / Rhiju Das / Kathleen Collins / Thi Hoang Duong Nguyen /
Abstract: Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere loss that is caused by incomplete genome end replication. In humans, telomerase is upregulated during embryogenesis ...Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere loss that is caused by incomplete genome end replication. In humans, telomerase is upregulated during embryogenesis and in cancers, and mutations that compromise the function of telomerase result in disease. A previous structure of human telomerase at a resolution of 8 Å revealed a vertebrate-specific composition and architecture, comprising a catalytic core that is flexibly tethered to an H and ACA (hereafter, H/ACA) box ribonucleoprotein (RNP) lobe by telomerase RNA. High-resolution structural information is necessary to develop treatments that can effectively modulate telomerase activity as a therapeutic approach against cancers and disease. Here we used cryo-electron microscopy to determine the structure of human telomerase holoenzyme bound to telomeric DNA at sub-4 Å resolution, which reveals crucial DNA- and RNA-binding interfaces in the active site of telomerase as well as the locations of mutations that alter telomerase activity. We identified a histone H2A-H2B dimer within the holoenzyme that was bound to an essential telomerase RNA motif, which suggests a role for histones in the folding and function of telomerase RNA. Furthermore, this structure of a eukaryotic H/ACA RNP reveals the molecular recognition of conserved RNA and protein motifs, as well as interactions that are crucial for understanding the molecular pathology of many mutations that cause disease. Our findings provide the structural details of the assembly and active site of human telomerase, which paves the way for the development of therapeutic agents that target this enzyme.
History
DepositionJan 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed ..._citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-12177
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12177
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
K: Telomerase Cajal body protein 1
G: H/ACA ribonucleoprotein complex subunit DKC1
J: H/ACA ribonucleoprotein complex subunit 3
B: RNA (92-MER)
H: H/ACA ribonucleoprotein complex subunit 1
I: H/ACA ribonucleoprotein complex subunit 2
D: H/ACA ribonucleoprotein complex subunit 1
F: H/ACA ribonucleoprotein complex subunit 3
E: H/ACA ribonucleoprotein complex subunit 2
C: H/ACA ribonucleoprotein complex subunit DKC1


Theoretical massNumber of molelcules
Total (without water)415,06110
Polymers415,06110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
H/ACA ribonucleoprotein complex subunit ... , 4 types, 8 molecules GCJFHDIE

#2: Protein H/ACA ribonucleoprotein complex subunit DKC1 / CBF5 homolog / Dyskerin / Nopp140-associated protein of 57 kDa / Nucleolar protein NAP57 / ...CBF5 homolog / Dyskerin / Nopp140-associated protein of 57 kDa / Nucleolar protein NAP57 / Nucleolar protein family A member 4 / snoRNP protein DKC1


Mass: 57779.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Organ: Kidney / Plasmid details: endogenous
References: UniProt: O60832, Isomerases; Intramolecular transferases; Transferring other groups
#3: Protein H/ACA ribonucleoprotein complex subunit 3 / Nucleolar protein 10 / Nucleolar protein family A member 3 / snoRNP protein NOP10


Mass: 7719.989 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Organ: Kidney / Plasmid details: endogenous / References: UniProt: Q9NPE3
#5: Protein H/ACA ribonucleoprotein complex subunit 1 / Nucleolar protein family A member 1 / snoRNP protein GAR1


Mass: 22387.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Organ: Kidney / References: UniProt: Q9NY12
#6: Protein H/ACA ribonucleoprotein complex subunit 2 / Nucleolar protein family A member 2 / snoRNP protein NHP2


Mass: 17226.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Organ: Kidney / References: UniProt: Q9NX24

-
Protein / RNA chain , 2 types, 2 molecules KB

#1: Protein Telomerase Cajal body protein 1 / WD repeat-containing protein 79 / WD40 repeat-containing protein antisense to TP53 gene / WRAP53beta


Mass: 59357.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293T / Organ: Kidney / Plasmid details: endogenous / References: UniProt: Q9BUR4
#4: RNA chain RNA (92-MER)


Mass: 145477.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293T / Organ: Kidney / Plasmid: pcDNA 3.1
Details (production host): pcDNA 3.1 inserted with U3 promoter-hTR gene-hepatitis virus D ribozyme
Cell line (production host): 293T / Organ (production host): kidney / Production host: Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Human telomerase H/ACA RNP lobeCOMPLEXThe hTR H/ACA motif, which adopts a double-hairpin structure hinged by the H-box and flanked by the ACA box, scaffolds the assembly of two copies each of dyskerin, NHP2, NOP10 and GAR1, one on each hairpin. TCAB1 binds the CAB box.all0MULTIPLE SOURCES
2ribonucleoprotein and telomerase complexCOMPLEX1,2,3,5,61NATURAL
3RNACOMPLEX41RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
32 mMmagnesium chlorideMgCl21
40.05 %Igepal CA630(C2H4O)nC14H22O1
51 %TrehaloseC12H22O111
61 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot for 4-5 seconds before plunging

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 78 K
Image recordingAverage exposure time: 1 sec. / Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 43639
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

SoftwareName: REFMAC / Version: 5.8.0256 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION3.1particle selectionAutomatic picking using 2D references
2SerialEMimage acquisition
4CTFFINDCTF correction
9REFMACmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
Image processingDetails: All images were processed using RELION 3.1.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15760434
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204665 / Symmetry type: POINT
Atomic model buildingB value: 104 / Protocol: AB INITIO MODEL / Space: RECIPROCAL
RefinementResolution: 3.4→3.4 Å / Cor.coef. Fo:Fc: 0.921 / SU B: 27.788 / SU ML: 0.378 / ESU R: 0.541
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.3045 --
obs0.3045 111019 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 229.966 Å2
Baniso -1Baniso -2Baniso -3
1--10.12 Å2-4.35 Å21.24 Å2
2--17.04 Å2-10.11 Å2
3----6.92 Å2
Refinement stepCycle: 1 / Total: 14538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.01815035
ELECTRON MICROSCOPYr_bond_other_d0.0030.0213141
ELECTRON MICROSCOPYr_angle_refined_deg1.5841.85720760
ELECTRON MICROSCOPYr_angle_other_deg1.18330583
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.02451559
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.20423.209561
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.13152335
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.76915103
ELECTRON MICROSCOPYr_chiral_restr0.0880.22295
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.02115059
ELECTRON MICROSCOPYr_gen_planes_other0.0030.023114
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it24.37522.026281
ELECTRON MICROSCOPYr_mcbond_other24.36722.0216280
ELECTRON MICROSCOPYr_mcangle_it34.64932.9757825
ELECTRON MICROSCOPYr_mcangle_other34.64932.9767826
ELECTRON MICROSCOPYr_scbond_it25.64324.4268754
ELECTRON MICROSCOPYr_scbond_other25.64224.4258755
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other37.20736.08112936
ELECTRON MICROSCOPYr_long_range_B_refined47.38354150
ELECTRON MICROSCOPYr_long_range_B_other47.38254149
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.39→3.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.882 8235 -
obs--100 %

+
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