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- EMDB-21567: Cryo-EM structure of CST bound to telomeric single-stranded DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-21567
TitleCryo-EM structure of CST bound to telomeric single-stranded DNA
Map dataMonomer map sharpened and mapped on D5 symmetry
Sample
  • Complex: Human CST complex
    • Protein or peptide: CST complex subunit CTC1
    • DNA: DNA (5'-D(P*TP*AP*GP*G)-3')
    • Protein or peptide: CST complex subunit STN1
    • Protein or peptide: CST complex subunit TEN1
  • Ligand: ZINC ION
Function / homology
Function and homology information


CST complex / telomerase inhibitor activity / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / G-rich strand telomeric DNA binding / single-stranded telomeric DNA binding / Polymerase switching on the C-strand of the telomere / telomere capping / bone marrow development / intermediate filament cytoskeleton ...CST complex / telomerase inhibitor activity / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / G-rich strand telomeric DNA binding / single-stranded telomeric DNA binding / Polymerase switching on the C-strand of the telomere / telomere capping / bone marrow development / intermediate filament cytoskeleton / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
CST complex subunit CTC1 / CST complex subunit TEN1 / CST complex subunit STN1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: 0.451
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.451
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w6w
  • Surface level: 0.451
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6w6w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21567.png

Downloads & links

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Map

FileDownload / File: emd_21567.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomer map sharpened and mapped on D5 symmetry
Voxel sizeX=Y=Z: 1.078 Å
Density
Contour LevelBy AUTHOR: 0.451 / Movie #1: 0.451
Minimum - Maximum-1.8611768 - 4.007554
Average (Standard dev.)0.0059442953 (±0.07369073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 431.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0781.0781.078
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z431.200431.200431.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.8614.0080.006

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Supplemental data

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Mask #1

Fileemd_21567_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 CST complex

EntireName: Human CST complex
Components
  • Complex: Human CST complex
    • Protein or peptide: CST complex subunit CTC1
    • DNA: DNA (5'-D(P*TP*AP*GP*G)-3')
    • Protein or peptide: CST complex subunit STN1
    • Protein or peptide: CST complex subunit TEN1
  • Ligand: ZINC ION

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Supramolecule #1: Human CST complex

SupramoleculeName: Human CST complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightExperimental: 200 KDa

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Macromolecule #1: CST complex subunit CTC1

MacromoleculeName: CST complex subunit CTC1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.745984 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDDDDKD YKDDDDKAAG RAQVPSSEQA WLEDAQVFIQ KTLCPAVKEP NVQLTPLVID CVKTVWLSQG RNQGSTLPLS YSFVSVQDL KTHQRLPCCS HLSWSSSAYQ AWAQEAGPNG NPLPREQLLL LGTLTDLSAD LEQECRNGSL YVRDNTGVLS C ELIDLDLS ...String:
MDYKDDDDKD YKDDDDKAAG RAQVPSSEQA WLEDAQVFIQ KTLCPAVKEP NVQLTPLVID CVKTVWLSQG RNQGSTLPLS YSFVSVQDL KTHQRLPCCS HLSWSSSAYQ AWAQEAGPNG NPLPREQLLL LGTLTDLSAD LEQECRNGSL YVRDNTGVLS C ELIDLDLS WLGHLFLFPR WSYLPPARWN SSGEGHLELW DAPVPVFPLT ISPGPVTPIP VLYPESASCL LRLRNKLRGV QR NLAGSLV RLSALVKSKQ KAYFILSLGR SHPAVTHVSI IVQVPAQLVW HRALRPGTAY VLTELRVSKI RGQRQHVWMT SQS SRLLLL KPECVQELEL ELEGPLLEAD PKPLPMPSNS EDKKDPESLV RYSRLLSYSG AVTGVLNEPA GLYELDGQLG LCLA YQQFR GLRRVMRPGV CLQLQDVHLL QSVGGGTRRP VLAPCLRGAV LLQSFSRQKP GAHSSRQAYG ASLYEQLVWE RQLGL PLYL WATKALEELA CKLCPHVLRH HQFLQHSSPG SPSLGLQLLA PTLDLLAPPG SPVRNAHNEI LEEPHHCPLQ KYTRLQ TPS SFPTLATLKE EGQRKAWASF DPKALLPLPE ASYLPSCQLN RRLAWSWLCL LPSAFCPAQV LLGVLVASSH KGCLQLR DQ SGSLPCLLLA KHSQPLSDPR LIGCLVRAER FQLIVERDVR SSFPSWKELS MPGFIQKQQA RVYVQFFLAD ALILPVPR P CLHSATPSTP QTDPTGPEGP HLGQSRLFLL CHKEALMKRN FCVPPGASPE VPKPALSFYV LGSWLGGTQR KEGTGWGLP EPQGNDDNDQ KVHLIFFGSS VRWFEFLHPG QVYRLIAPGP ATPMLFEKDG SSCISRRPLE LAGCASCLTV QDNWTLELES SQDIQDVLD ANKSLPESSL TDLLSDNFTD SLVSFSAEIL SRTLCEPLVA SLWMKLGNTG AMRRCVKLTV ALETAECEFP P HLDVYIED PHLPPSLGLL PGARVHFSQL EKRVSRSHNV YCCFRSSTYV QVLSFPPETT ISIPLPHIYL AELLQGGQSP FQ ATASCHI VSVFSLQLFW VCAYCTSICR QGKCTRLGST CPTQTAISQA IIRLLVEDGT AEAVVTCRNH HVAAALGLCP REW ASLLDF VQVPGRVVLQ FAGPGAQLES SARVDEPMTM FLWTLCTSPS VLRPIVLSFE LERKPSKIVP LEPPRLQRFQ CGEL PFLTH VNPRLRLSCL SIRESEYSSS LGILASSC

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Macromolecule #3: CST complex subunit STN1

MacromoleculeName: CST complex subunit STN1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.001824 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHQPG SSRCEEETPS LLWGLDPVFL AFAKLYIRDI LDMKESRQVP GVFLYNGHPI KQVDVLGTVI GVRERDAFYS YGVDDSTGV INCICWKKLN TESVSAAPSA ARELSLTSQL KKLQETIEQK TKIEIGDTIR VRGSIRTYRE EREIHATTYY K VDDPVWNI ...String:
MHHHHHHQPG SSRCEEETPS LLWGLDPVFL AFAKLYIRDI LDMKESRQVP GVFLYNGHPI KQVDVLGTVI GVRERDAFYS YGVDDSTGV INCICWKKLN TESVSAAPSA ARELSLTSQL KKLQETIEQK TKIEIGDTIR VRGSIRTYRE EREIHATTYY K VDDPVWNI QIARMLELPT IYRKVYDQPF HSSALEKEEA LSNPGALDLP SLTSLLSEKA KEFLMENRVQ SFYQQELEMV ES LLSLANQ PVIHSASSDQ VNFKKDTTSK AIHSIFKNAI QLLQEKGLVF QKDDGFDNLY YVTREDKDLH RKIHRIIQQD CQK PNHMEK GCHFLHILAC ARLSIRPGLS EAVLQQVLEL LEDQSDIVST MEHYYTAF

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Macromolecule #4: CST complex subunit TEN1

MacromoleculeName: CST complex subunit TEN1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.285604 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSYYHHHHHH DYDIPTTENL YFQGAMGSGI QLPKPGTYYL PWEVSAGQVP DGSTLRTFGR LCLYDMIQSR VTLMAQHGSD QHQVLVCTK LVEPFHAQVG SLYIVLGELQ HQQDRGSVVK ARVLTCVEGM NLPLLEQAIR EQRLYKQERG GSQ

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Macromolecule #2: DNA (5'-D(P*TP*AP*GP*G)-3')

MacromoleculeName: DNA (5'-D(P*TP*AP*GP*G)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.230854 KDa
SequenceString:
(DT)(DA)(DG)(DG)

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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 TITAN KRIOS
Electron beamAcceleration voltage: 300 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: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSparc2 ab initio program
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 833627
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5w2l

chain_id: A

4joi

chain_id: A

4joi

chain_id: C

4jqf

chain_id: A
RefinementProtocol: AB INITIO MODEL
Output model

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

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