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- PDB-6w6w: Cryo-EM structure of CST bound to telomeric single-stranded DNA -

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Basic information

Entry
Database: PDB / ID: 6w6w
TitleCryo-EM structure of CST bound to telomeric single-stranded DNA
Components
  • CST complex subunit CTC1
  • CST complex subunit STN1
  • CST complex subunit TEN1
  • DNA (5'-D(P*TP*AP*GP*G)-3')
KeywordsSTRUCTURAL PROTEIN/DNA / Telomere homeostasis / telomere packaging / telomerase terminator / DNA replication / Double-stranded breaks repair / single-stranded DNA-binding proteins / higher-order protein assembly / DNA-induced oligomeriization / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


CST complex / telomerase inhibitor activity / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / single-stranded telomeric DNA binding / intermediate filament cytoskeleton / G-rich strand telomeric DNA binding / telomere capping / Polymerase switching on the C-strand of the telomere / bone marrow development ...CST complex / telomerase inhibitor activity / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / single-stranded telomeric DNA binding / intermediate filament cytoskeleton / G-rich strand telomeric DNA binding / telomere capping / Polymerase switching on the C-strand of the telomere / bone marrow development / hematopoietic stem cell proliferation / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / replicative senescence / spleen development / regulation of G2/M transition of mitotic cell cycle / telomere maintenance / thymus development / positive regulation of DNA replication / multicellular organism growth / fibrillar center / positive regulation of fibroblast proliferation / single-stranded DNA binding / chromosome, telomeric region / intracellular membrane-bounded organelle / DNA damage response / nucleoplasm / nucleus / cytosol
Similarity search - Function
CST complex subunit Ten1, animal and plant type / CST complex subunit CTC1 / CST complex subunit CTC1-like / CST, telomere maintenance, complex subunit CTC1 / Telomere-capping, CST complex subunit / CST complex subunit Stn1 / Stn1, C-terminal / CST complex subunit Stn1, wHTH1 motif superfamily / CST, complex subunit STN1, C terminal / Replication factor A protein-like ...CST complex subunit Ten1, animal and plant type / CST complex subunit CTC1 / CST complex subunit CTC1-like / CST, telomere maintenance, complex subunit CTC1 / Telomere-capping, CST complex subunit / CST complex subunit Stn1 / Stn1, C-terminal / CST complex subunit Stn1, wHTH1 motif superfamily / CST, complex subunit STN1, C terminal / Replication factor A protein-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / CST complex subunit CTC1 / CST complex subunit TEN1 / CST complex subunit STN1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLim, C. / Barbour, A.T. / Zaug, A.J. / Goodrich, K.J. / McKay, A.E. / Wuttke, D.S. / Cech, T.R.
Funding support United States, 6items
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)R01GM099705 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)K99GM131023 United States
National Science Foundation (NSF, United States)MCB 1716425 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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: CST complex subunit CTC1
E: DNA (5'-D(P*TP*AP*GP*G)-3')
B: CST complex subunit CTC1
C: CST complex subunit STN1
D: CST complex subunit TEN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,0766
Polymers335,0105
Non-polymers651
Water00
1


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

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Components

#1: Protein CST complex subunit CTC1 / Conserved telomere maintenance component 1 / HBV DNAPTP1-transactivated protein B


Mass: 136745.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTC1, C17orf68 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2NKJ3
#2: DNA chain DNA (5'-D(P*TP*AP*GP*G)-3')


Mass: 1230.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein CST complex subunit STN1 / Oligonucleotide/oligosaccharide-binding fold-containing protein 1 / Suppressor of cdc thirteen homolog


Mass: 43001.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STN1, OBFC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H668
#4: Protein CST complex subunit TEN1 / Protein telomeric pathways with STN1 homolog / Telomere length regulation protein TEN1 homolog


Mass: 17285.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEN1, C17orf106 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86WV5
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human CST complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
12cryoSPARC23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 833627 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
15W2L

5w2l

A5W2L1
24JOI

4joi

A4JOI2
34JOI

4joi

C4JOI2
44JQF

4jqf

A4JQF3

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