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- EMDB-21565: Arm conformation from CST-3xTEL oligomer-mixture -

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Basic information

Entry
Database: EMDB / ID: EMD-21565
TitleArm conformation from CST-3xTEL oligomer-mixture
Map dataArm conformation from CST-3xTEL oligomer-mixture
Sample
  • Complex: Arm conformation of CST monomer from CST-3xTEL oligomer-mixture
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsLim C / Barbour AT / Zaug AJ / Goodrich KJ / McKay AE / Wuttke DS / Cech TR
Funding support United States, 6 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Tom Cech HHMI Investigator United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM059414 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM099705 United States
National Science Foundation (NSF, United States)MCB 1716425 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM131023 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008759 United States
CitationJournal: Science / Year: 2020
Title: The structure of human CST reveals a decameric assembly bound to telomeric DNA.
Authors: Ci Ji Lim / Alexandra T Barbour / Arthur J Zaug / Karen J Goodrich / Allison E McKay / Deborah S Wuttke / Thomas R Cech /
Abstract: The CTC1-STN1-TEN1 (CST) complex is essential for telomere maintenance and resolution of stalled replication forks genome-wide. Here, we report the 3.0-angstrom cryo-electron microscopy structure of ...The CTC1-STN1-TEN1 (CST) complex is essential for telomere maintenance and resolution of stalled replication forks genome-wide. Here, we report the 3.0-angstrom cryo-electron microscopy structure of human CST bound to telomeric single-stranded DNA (ssDNA), which assembles as a decameric supercomplex. The atomic model of the 134-kilodalton CTC1 subunit, built almost entirely de novo, reveals the overall architecture of CST and the DNA-binding anchor site. The carboxyl-terminal domain of STN1 interacts with CTC1 at two separate docking sites, allowing allosteric mediation of CST decamer assembly. Furthermore, ssDNA appears to staple two monomers to nucleate decamer assembly. CTC1 has stronger structural similarity to Replication Protein A than the expected similarity to yeast Cdc13. The decameric structure suggests that CST can organize ssDNA analogously to the nucleosome's organization of double-stranded DNA.
History
DepositionMar 17, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateJun 17, 2020-
Current statusJun 17, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0142
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0142
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21565.png

Downloads & links

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Map

FileDownload / File: emd_21565.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArm conformation from CST-3xTEL oligomer-mixture
Voxel sizeX=Y=Z: 1.219 Å
Density
Contour LevelBy AUTHOR: 0.0142 / Movie #1: 0.0142
Minimum - Maximum-0.010688402 - 0.046140924
Average (Standard dev.)0.0002722962 (±0.0023292215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 312.064 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2191.2191.219
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z312.064312.064312.064
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0110.0460.000

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Supplemental data

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Sample components

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Entire : Arm conformation of CST monomer from CST-3xTEL oligomer-mixture

EntireName: Arm conformation of CST monomer from CST-3xTEL oligomer-mixture
Components
  • Complex: Arm conformation of CST monomer from CST-3xTEL oligomer-mixture

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Supramolecule #1: Arm conformation of CST monomer from CST-3xTEL oligomer-mixture

SupramoleculeName: Arm conformation of CST monomer from CST-3xTEL oligomer-mixture
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightExperimental: 200 KDa

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSparc2 ab initio reconstruction program
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number images used: 51811
FSC plot (resolution estimation)

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