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- EMDB-7519: The H/ACA ribonucleoprotein lobe of the cryo-EM structure of subs... -

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Basic information

Entry
Database: EMDB / ID: EMD-7519
TitleThe H/ACA ribonucleoprotein lobe of the cryo-EM structure of substrate-bound human telomerase holoenzyme
Map dataThe H/ACA RNP lobe of the human telomerase holoenzyme
Sample
  • Complex: Human telomerase holoenzyme in complex with DNA substrate
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsNguyen THD / Tam J / Wu RA / Greber BJ / Toso D / Nogales E / Collins K
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of substrate-bound human telomerase holoenzyme.
Authors: Thi Hoang Duong Nguyen / Jane Tam / Robert A Wu / Basil J Greber / Daniel Toso / Eva Nogales / Kathleen Collins /
Abstract: The enzyme telomerase adds telomeric repeats to chromosome ends to balance the loss of telomeres during genome replication. Telomerase regulation has been implicated in cancer, other human diseases, ...The enzyme telomerase adds telomeric repeats to chromosome ends to balance the loss of telomeres during genome replication. Telomerase regulation has been implicated in cancer, other human diseases, and ageing, but progress towards clinical manipulation of telomerase has been hampered by the lack of structural data. Here we present the cryo-electron microscopy structure of the substrate-bound human telomerase holoenzyme at subnanometre resolution, showing two flexibly RNA-tethered lobes: the catalytic core with telomerase reverse transcriptase (TERT) and conserved motifs of telomerase RNA (hTR), and an H/ACA ribonucleoprotein (RNP). In the catalytic core, RNA encircles TERT, adopting a well-ordered tertiary structure with surprisingly limited protein-RNA interactions. The H/ACA RNP lobe comprises two sets of heterotetrameric H/ACA proteins and one Cajal body protein, TCAB1, representing a pioneering structure of a large eukaryotic family of ribosome and spliceosome biogenesis factors. Our findings provide a structural framework for understanding human telomerase disease mutations and represent an important step towards telomerase-related clinical therapeutics.
History
DepositionMar 5, 2018-
Header (metadata) releaseMar 21, 2018-
Map releaseMay 2, 2018-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7519.png

Downloads & links

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Map

FileDownload / File: emd_7519.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe H/ACA RNP lobe of the human telomerase holoenzyme
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.047446378 - 0.17658517
Average (Standard dev.)0.00015894054 (±0.0022785873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 460.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z460.000460.000460.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0470.1770.000

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Supplemental data

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Mask #1

Fileemd_7519_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human telomerase holoenzyme in complex with DNA substrate

EntireName: Human telomerase holoenzyme in complex with DNA substrate
Components
  • Complex: Human telomerase holoenzyme in complex with DNA substrate

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Supramolecule #1: Human telomerase holoenzyme in complex with DNA substrate

SupramoleculeName: Human telomerase holoenzyme in complex with DNA substrate
type: complex / ID: 1 / Parent: 0 / Details: Sample was purified from human cells
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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: 8
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 11654 / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.0) / Details: RELION maximum likelihood
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.0) / Details: RELION maximum likelihood
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 36210
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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