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- PDB-8soj: Cryo-EM structure of human CST bound to POT1(ESDL)/TPP1 in the ab... -

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Basic information

Entry
Database: PDB / ID: 8soj
TitleCryo-EM structure of human CST bound to POT1(ESDL)/TPP1 in the absence of telomeric ssDNA
Components
  • CST complex subunit CTC1
  • CST complex subunit STN1
  • CST complex subunit TEN1
  • Protection of telomeres protein 1
KeywordsDNA BINDING PROTEIN / telomere / shelterin / cst / complex
Function / homology
Function and homology information


positive regulation of DNA strand elongation / positive regulation of telomeric D-loop disassembly / G-rich single-stranded DNA binding / CST complex / telomere assembly / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of double-strand break repair via nonhomologous end joining ...positive regulation of DNA strand elongation / positive regulation of telomeric D-loop disassembly / G-rich single-stranded DNA binding / CST complex / telomere assembly / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of double-strand break repair via nonhomologous end joining / protection from non-homologous end joining at telomere / DEAD/H-box RNA helicase binding / telomerase inhibitor activity / establishment of protein localization to telomere / regulation of establishment of protein localization to telomere / telomeric D-loop disassembly / shelterin complex / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / telomere capping / intermediate filament cytoskeleton / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / telomerase holoenzyme complex / Removal of the Flap Intermediate from the C-strand / bone marrow development / embryonic limb morphogenesis / protein localization to chromosome, telomeric region / telomeric DNA binding / hematopoietic stem cell proliferation / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / replicative senescence / Telomere Extension By Telomerase / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / telomere maintenance via telomerase / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / spleen development / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / regulation of G2/M transition of mitotic cell cycle / Packaging Of Telomere Ends / DNA polymerase binding / positive regulation of telomere maintenance via telomerase / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / bioluminescence / thymus development / positive regulation of DNA replication / skeletal system development / picornain 2A / generation of precursor metabolites and energy / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / intracellular protein transport / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / DNA Damage/Telomere Stress Induced Senescence / multicellular organism growth / fibrillar center / positive regulation of fibroblast proliferation / single-stranded DNA binding / nucleoside-triphosphate phosphatase / outer membrane-bounded periplasmic space / channel activity / monoatomic ion transmembrane transport / chromosome, telomeric region / DNA replication / RNA helicase activity / nuclear body / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / intracellular membrane-bounded organelle / DNA-templated transcription / DNA damage response / protein-containing complex binding / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding
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 / : ...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 / : / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Replication factor A protein-like / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Winged helix DNA-binding domain superfamily / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Winged helix-like DNA-binding domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Maltose/maltodextrin-binding periplasmic protein / CST complex subunit CTC1 / CST complex subunit TEN1 / Adrenocortical dysplasia protein homolog / CST complex subunit STN1 / Protection of telomeres protein 1
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
Human enterovirus 71
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsCai, S.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Other privateBCRF-22-036
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA210036 United States
Citation
Journal: Cell / Year: 2024
Title: POT1 recruits and regulates CST-Polα/primase at human telomeres.
Authors: Sarah W Cai / Hiroyuki Takai / Arthur J Zaug / Teague C Dilgen / Thomas R Cech / Thomas Walz / Titia de Lange /
Abstract: Telomere maintenance requires the extension of the G-rich telomeric repeat strand by telomerase and the fill-in synthesis of the C-rich strand by Polα/primase. At telomeres, Polα/primase is bound ...Telomere maintenance requires the extension of the G-rich telomeric repeat strand by telomerase and the fill-in synthesis of the C-rich strand by Polα/primase. At telomeres, Polα/primase is bound to Ctc1/Stn1/Ten1 (CST), a single-stranded DNA-binding complex. Like mutations in telomerase, mutations affecting CST-Polα/primase result in pathological telomere shortening and cause a telomere biology disorder, Coats plus (CP). We determined cryogenic electron microscopy structures of human CST bound to the shelterin heterodimer POT1/TPP1 that reveal how CST is recruited to telomeres by POT1. Our findings suggest that POT1 hinge phosphorylation is required for CST recruitment, and the complex is formed through conserved interactions involving several residues mutated in CP. Our structural and biochemical data suggest that phosphorylated POT1 holds CST-Polα/primase in an inactive, autoinhibited state until telomerase has extended the telomere ends. We propose that dephosphorylation of POT1 releases CST-Polα/primase into an active state that completes telomere replication through fill-in synthesis.
#1: Journal: bioRxiv / Year: 2023
Title: POT1 recruits and regulates CST-Polα/Primase at human telomeres.
Authors: Sarah W Cai / Hiroyuki Takai / Thomas Walz / Titia de Lange /
Abstract: Telomere maintenance requires extension of the G-rich telomeric repeat strand by telomerase and fill-in synthesis of the C-rich strand by Polα/Primase. Telomeric Polα/Primase is bound to Ctc1-Stn1- ...Telomere maintenance requires extension of the G-rich telomeric repeat strand by telomerase and fill-in synthesis of the C-rich strand by Polα/Primase. Telomeric Polα/Primase is bound to Ctc1-Stn1-Ten1 (CST), a single-stranded DNA-binding complex. Like mutations in telomerase, mutations affecting CST-Polα/Primase result in pathological telomere shortening and cause a telomere biology disorder, Coats plus (CP). We determined cryogenic electron microscopy structures of human CST bound to the shelterin heterodimer POT1/TPP1 that reveal how CST is recruited to telomeres by POT1. Phosphorylation of POT1 is required for CST recruitment, and the complex is formed through conserved interactions involving several residues mutated in CP. Our structural and biochemical data suggest that phosphorylated POT1 holds CST-Polα/Primase in an inactive auto-inhibited state until telomerase has extended the telomere ends. We propose that dephosphorylation of POT1 releases CST-Polα/Primase into an active state that completes telomere replication through fill-in synthesis.
History
DepositionApr 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CST complex subunit CTC1
B: CST complex subunit STN1
C: CST complex subunit TEN1
D: Protection of telomeres protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,8696
Polymers380,7384
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CST complex subunit CTC1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Conserved telomere ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Conserved telomere maintenance component 1 / HBV DNAPTP1-transactivated protein B


Mass: 178300.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His6-MBP-3C tagged human Ctc1
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, CTC1, C17orf68 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0AEY0, UniProt: Q2NKJ3
#2: Protein CST complex subunit STN1 / POT1 and TIN2-interacting protein / Oligonucleotide/oligosaccharide-binding fold-containing protein ...POT1 and TIN2-interacting protein / Oligonucleotide/oligosaccharide-binding fold-containing protein 1 / Suppressor of cdc thirteen homolog


Mass: 115627.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71, (gene. exp.) Homo sapiens (human)
Gene: ACD, PIP1, PTOP, TINT1, TPP1, STN1, OBFC1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: B6F2F5, UniProt: Q96AP0, UniProt: Q9H668, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein CST complex subunit TEN1 / Protein telomeric pathways with STN1 homolog / Telomere length regulation protein TEN1 homolog


Mass: 13872.013 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
#4: Protein Protection of telomeres protein 1 / hPot1 / POT1-like telomere end-binding protein


Mass: 72938.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mPOT1b residues ESDL 323-326 are inserted into the human POT1 sequence between S320 and V321
Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NUX5
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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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-POT1(ESDL)/TPP1 complex / Type: COMPLEX / Details: CST-POT1(ESDL)/TPP1 complex in the absence of DNA / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.38 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenConc.: 0.05 mg/ml / Embedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132356 / Symmetry type: POINT
RefinementCross valid method: NONE

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