[English] 日本語
Yorodumi
- EMDB-26346: Cryo-EM structure of human CST bound to DNA polymerase alpha-prim... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26346
TitleCryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state
Map dataHuman CST-Pol alpha/Primase bound to ssDNA in a recruitment state.
Sample
  • Complex: Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in a recruitment state
    • Protein or peptide: DNA primase small subunitPrimase
    • Protein or peptide: DNA primase large subunitPrimase
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Protein or peptide: DNA polymerase alpha subunit BDNA polymerase
    • Protein or peptide: CST complex subunit CTC1
    • Protein or peptide: CST complex subunit STN1
    • Protein or peptide: CST complex subunit TEN1
    • DNA: canonical telomeric DNA sequence
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
KeywordsFill-in / Telomere / Replication / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


CST complex / DNA primase AEP / positive regulation of DNA primase activity / ribonucleotide binding / telomerase inhibitor activity / DNA replication initiation / DNA/RNA hybrid binding / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 ...CST complex / DNA primase AEP / positive regulation of DNA primase activity / ribonucleotide binding / telomerase inhibitor activity / DNA replication initiation / DNA/RNA hybrid binding / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / regulation of type I interferon production / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / single-stranded telomeric DNA binding / DNA primase activity / Polymerase switching on the C-strand of the telomere / lagging strand elongation / mitotic DNA replication initiation / DNA replication, synthesis of primer / telomere capping / bone marrow development / intermediate filament cytoskeleton / DNA strand elongation involved in DNA replication / hematopoietic stem cell proliferation / leading strand elongation / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / telomeric DNA binding / DNA replication origin binding / negative regulation of telomere maintenance via telomerase / DNA replication initiation / replicative senescence / Activation of the pre-replicative complex / spleen development / regulation of G2/M transition of mitotic cell cycle / telomere maintenance / thymus development / positive regulation of DNA replication / Defective pyroptosis / multicellular organism growth / fibrillar center / nuclear matrix / double-strand break repair via nonhomologous end joining / protein import into nucleus / positive regulation of fibroblast proliferation / single-stranded DNA binding / nuclear envelope / 4 iron, 4 sulfur cluster binding / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA repair / intracellular membrane-bounded organelle / DNA damage response / chromatin binding / chromatin / nucleolus / protein kinase binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / metal ion binding / 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 / DNA polymerase alpha, subunit B, N-terminal domain superfamily / DNA polymerase alpha subunit B N-terminal / DNA polymerase alpha, subunit B, N-terminal / DNA polymerase alpha, subunit B / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / Eukaryotic and archaeal DNA primase, large subunit / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit / DNA primase small subunit / DNA primase large subunit / DNA polymerase alpha subunit B / 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: 4.6 Å
AuthorsCai SW / Zinder JC / Svetlov V / Bush MW / Nudler E / Walz T / de Lange T
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5 R35 CA210036 United States
Breast Cancer Research FoundationBCRF-19-036 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Cryo-EM structure of the human CST-Polα/primase complex in a recruitment state.
Authors: Sarah W Cai / John C Zinder / Vladimir Svetlov / Martin W Bush / Evgeny Nudler / Thomas Walz / Titia de Lange /
Abstract: The CST-Polα/primase complex is essential for telomere maintenance and functions to counteract resection at double-strand breaks. We report a 4.6-Å resolution cryo-EM structure of human CST- ...The CST-Polα/primase complex is essential for telomere maintenance and functions to counteract resection at double-strand breaks. We report a 4.6-Å resolution cryo-EM structure of human CST-Polα/primase, captured prior to catalysis in a recruitment state stabilized by chemical cross-linking. Our structure reveals an evolutionarily conserved interaction between the C-terminal domain of the catalytic POLA1 subunit and an N-terminal expansion in metazoan CTC1. Cross-linking mass spectrometry and negative-stain EM analysis provide insight into CST binding by the flexible POLA1 N-terminus. Finally, Coats plus syndrome disease mutations previously characterized to disrupt formation of the CST-Polα/primase complex map to protein-protein interfaces observed in the recruitment state. Together, our results shed light on the architecture and stoichiometry of the metazoan fill-in machinery.
History
DepositionMar 2, 2022-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26346.png

Downloads & links

-
Map

FileDownload / File: emd_26346.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman CST-Pol alpha/Primase bound to ssDNA in a recruitment state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.041180167 - 0.084259294
Average (Standard dev.)0.000015990241 (±0.0018551061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_26346_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_26346_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in...

EntireName: Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in a recruitment state
Components
  • Complex: Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in a recruitment state
    • Protein or peptide: DNA primase small subunitPrimase
    • Protein or peptide: DNA primase large subunitPrimase
    • Protein or peptide: DNA polymerase alpha catalytic subunit
    • Protein or peptide: DNA polymerase alpha subunit BDNA polymerase
    • Protein or peptide: CST complex subunit CTC1
    • Protein or peptide: CST complex subunit STN1
    • Protein or peptide: CST complex subunit TEN1
    • DNA: canonical telomeric DNA sequence
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster

+
Supramolecule #1: Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in...

SupramoleculeName: Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in a recruitment state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Details: Sample was GraFix cross-linked with glutaraldehyde.
Molecular weightTheoretical: 500 KDa

+
Macromolecule #1: DNA primase small subunit

MacromoleculeName: DNA primase small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.981012 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: METFDPTELP ELLKLYYRRL FPYSQYYRWL NYGGVIKNYF QHREFSFTLK DDIYIRYQSF NNQSDLEKEM QKMNPYKIDI GAVYSHRPN QHNTVKLGAF QAQEKELVFD IDMTDYDDVR RCCSSADICP KCWTLMTMAI RIIDRALKED FGFKHRLWVY S GRRGVHCW ...String:
METFDPTELP ELLKLYYRRL FPYSQYYRWL NYGGVIKNYF QHREFSFTLK DDIYIRYQSF NNQSDLEKEM QKMNPYKIDI GAVYSHRPN QHNTVKLGAF QAQEKELVFD IDMTDYDDVR RCCSSADICP KCWTLMTMAI RIIDRALKED FGFKHRLWVY S GRRGVHCW VCDESVRKLS SAVRSGIVEY LSLVKGGQDV KKKVHLSEKI HPFIRKSINI IKKYFEEYAL VNQDILENKE SW DKILALV PETIHDELQQ SFQKSHNSLQ RWEHLKKVAS RYQNNIKNDK YGPWLEWEIM LQYCFPRLDI NVSKGINHLL KSP FSVHPK TGRISVPIDL QKVDQFDPFT VPTISFICRE LDAISTNEEE KEENEAESDV KHRTRDYKKT SLAPYVKVFE HFLE NLDKS RKGELLKKSD LQKDF

UniProtKB: DNA primase small subunit

+
Macromolecule #2: DNA primase large subunit

MacromoleculeName: DNA primase large subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.092102 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGSMEFSGRK WRKLRLAGDQ RNASYPHCLQ FYLQPPSENI SLIEFENLAI DRVKLLKSVE NLGVSYVKGT EQYQSKLESE LRKLKFSYR ENLEDEYEPR RRDHISHFIL RLAYCQSEEL RRWFIQQEMD LLRFRFSILP KDKIQDFLKD SQLQFEAISD E EKTLREQE ...String:
GGSMEFSGRK WRKLRLAGDQ RNASYPHCLQ FYLQPPSENI SLIEFENLAI DRVKLLKSVE NLGVSYVKGT EQYQSKLESE LRKLKFSYR ENLEDEYEPR RRDHISHFIL RLAYCQSEEL RRWFIQQEMD LLRFRFSILP KDKIQDFLKD SQLQFEAISD E EKTLREQE IVASSPSLSG LKLGFESIYK IPFADALDLF RGRKVYLEDG FAYVPLKDIV AIILNEFRAK LSKALALTAR SL PAVQSDE RLQPLLNHLS HSYTGQDYST QGNVGKISLD QIDLLSTKSF PPCMRQLHKA LRENHHLRHG GRMQYGLFLK GIG LTLEQA LQFWKQEFIK GKMDPDKFDK GYSYNIRHSF GKEGKRTDYT PFSCLKIILS NPPSQGDYHG CPFRHSDPEL LKQK LQSYK ISPGGISQIL DLVKGTHYQV ACQKYFEMIH NVDDCGFSLN HPNQFFCESQ RILNGGKDIK KEPIQPETPQ PKPSV QKTK DASSALASLN SSLEMDMEGL EDYFSEDS

UniProtKB: DNA primase large subunit

+
Macromolecule #3: DNA polymerase alpha catalytic subunit

MacromoleculeName: DNA polymerase alpha catalytic subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.635125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPGSADEEQV FHFYWLDAYE DQYNQPGVVF LFGKVWIESA ETHVSCCVMV KNIERTLYFL PREMKIDLNT GKETGTPISM KDVYEEFDE KIATKYKIMK FKSKPVEKNY AFEIPDVPEK SEYLEVKYSA EMPQLPQDLK GETFSHVFGT NTSSLELFLM N RKIKGPCW ...String:
GPGSADEEQV FHFYWLDAYE DQYNQPGVVF LFGKVWIESA ETHVSCCVMV KNIERTLYFL PREMKIDLNT GKETGTPISM KDVYEEFDE KIATKYKIMK FKSKPVEKNY AFEIPDVPEK SEYLEVKYSA EMPQLPQDLK GETFSHVFGT NTSSLELFLM N RKIKGPCW LEVKSPQLLN QPVSWCKVEA MALKPDLVNV IKDVSPPPLV VMAFSMKTMQ NAKNHQNEII AMAALVHHSF AL DKAAPKP PFQSHFCVVS KPKDCIFPYA FKEVIEKKNV KVEVAATERT LLGFFLAKVH KIDPDIIVGH NIYGFELEVL LQR INVCKA PHWSKIGRLK RSNMPKLGGR SGFGERNATC GRMICDVEIS AKELIRCKSY HLSELVQQIL KTERVVIPME NIQN MYSES SQLLYLLEHT WKDAKFILQI MCELNVLPLA LQITNIAGNI MSRTLMGGRS ERNEFLLLHA FYENNYIVPD KQIFR KPQQ KLGDEDEEID GDTNKYKKGR KKAAYAGGLV LDPKVGFYDK FILLLDFNSL YPSIIQEFNI CFTTVQRVAS EAQKVT EDG EQEQIPELPD PSLEMGILPR EIRKLVERRK QVKQLMKQQD LNPDLILQYD IRQKALKLTA NSMYGCLGFS YSRFYAK PL AALVTYKGRE ILMHTKEMVQ KMNLEVIYGD TDSIMINTNS TNLEEVFKLG NKVKSEVNKL YKLLEIDIDG VFKSLLLL K KKKYAALVVE PTSDGNYVTK QELKGLDIVR RDWCDLAKDT GNFVIGQILS DQSRDTIVEN IQKRLIEIGE NVLNGSVPV SQFEINKALT KDPQDYPDKK SLPHVHVALW INSQGGRKVK AGDTVSYVIC QDGSNLTASQ RAYAPEQLQK QDNLTIDTQY YLAQQIHPV VARICEPIDG IDAVLIATWL GLDPTQFRVH HYHKDEENDA LLGGPAQLTD EEKYRDCERF KCPCPTCGTE N IYDNVFDG SGTDMEPSLY RCSNIDCKAS PLTFTVQLSN KLIMDIRRFI KKYYDGWLIC EEPTCRNRTR HLPLQFSRTG PL CPACMKA TLQPEYSDKS LYTQLCFYRY IFDAECALEK LTTDHEKDKL KKQFFTPKVL QDYRKLKNTA EQFLSRSGYS EVN LSKLFA GCAVKS

UniProtKB: DNA polymerase alpha catalytic subunit

+
Macromolecule #4: DNA polymerase alpha subunit B

MacromoleculeName: DNA polymerase alpha subunit B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.015539 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSASAQQLAE ELQIFGLDCE EALIEKLVEL CVQYGQNEEG MVGELIAFCT STHKVGLTSE ILNSFEHEFL SKRLSKARHS TCKDSGHAG ARDIVSIQEL IEVEEEEEIL LNSYTTPSKG SQKRAISTPE TPLTKRSVST RSPHQLLSPS SFSPSATPSQ K YNSRSNRG ...String:
MSASAQQLAE ELQIFGLDCE EALIEKLVEL CVQYGQNEEG MVGELIAFCT STHKVGLTSE ILNSFEHEFL SKRLSKARHS TCKDSGHAG ARDIVSIQEL IEVEEEEEIL LNSYTTPSKG SQKRAISTPE TPLTKRSVST RSPHQLLSPS SFSPSATPSQ K YNSRSNRG EVVTSFGLAQ GVSWSGRGGA GNISLKVLGC PEALTGSYKS MFQKLPDIRE VLTCKIEELG SELKEHYKIE AF TPLLAPA QEPVTLLGQI GCDSNGKLNN KSVILEGDRE HSSGAQIPVD LSELKEYSLF PGQVVIMEGI NTTGRKLVAT KLY EGVPLP FYQPTEEDAD FEQSMVLVAC GPYTTSDSIT YDPLLDLIAV INHDRPDVCI LFGPFLDAKH EQVENCLLTS PFED IFKQC LRTIIEGTRS SGSHLVFVPS LRDVHHEPVY PQPPFSYSDL SREDKKQVQF VSEPCSLSIN GVIFGLTSTD LLFHL GAEE ISSSSGTSDR FSRILKHILT QRSYYPLYPP QEDMAIDYES FYVYAQLPVT PDVLIIPSEL RYFVKDVLGC VCVNPG RLT KGQVGGTFAR LYLRRPAADG AERQSPCIAV QVVRI

UniProtKB: DNA polymerase alpha subunit B

+
Macromolecule #5: CST complex subunit CTC1

MacromoleculeName: CST complex subunit CTC1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.050328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPGSMAAGRA QVPSSEQAWL EDAQVFIQKT LCPAVKEPNV QLTPLVIDCV KTVWLSQGRN QGSTLPLSYS FVSVQDLKTH QRLPCCSHL SWSSSAYQAW AQEAGPNGNP LPREQLLLLG TLTDLSADLE QECRNGSLYV RDNTGVLSCE LIDLDLSWLG H LFLFPRWS ...String:
GPGSMAAGRA QVPSSEQAWL EDAQVFIQKT LCPAVKEPNV QLTPLVIDCV KTVWLSQGRN QGSTLPLSYS FVSVQDLKTH QRLPCCSHL SWSSSAYQAW AQEAGPNGNP LPREQLLLLG TLTDLSADLE QECRNGSLYV RDNTGVLSCE LIDLDLSWLG H LFLFPRWS YLPPARWNSS GEGHLELWDA PVPVFPLTIS PGPVTPIPVL YPESASCLLR LRNKLRGVQR NLAGSLVRLS AL VKSKQKA YFILSLGRSH PAVTHVSIIV QVPAQLVWHR ALRPGTAYVL TELRVSKIRG QRQHVWMTSQ SSRLLLLKPE CVQ ELELEL EGPLLEADPK PLPMPSNSED KKDPESLVRY SRLLSYSGAV TGVLNEPAGL YELDGQLGLC LAYQQFRGLR RVMR PGVCL QLQDVHLLQS VGGGTRRPVL APCLRGAVLL QSFSRQKPGA HSSRQAYGAS LYEQLVWERQ LGLPLYLWAT KALEE LACK LCPHVLRHHQ FLQHSSPGSP SLGLQLLAPT LDLLAPPGSP VRNAHNEILE EPHHCPLQKY TRLQTPSSFP TLATLK EEG QRKAWASFDP KALLPLPEAS YLPSCQLNRR LAWSWLCLLP SAFCPAQVLL GVLVASSHKG CLQLRDQSGS LPCLLLA KH SQPLSDPRLI GCLVRAERFQ LIVERDVRSS FPSWKELSMP GFIQKQQARV YVQFFLADAL ILPVPRPCLH SATPSTPQ T DPTGPEGPHL GQSRLFLLCH KEALMKRNFC VPPGASPEVP KPALSFYVLG SWLGGTQRKE GTGWGLPEPQ GNDDNDQKV HLIFFGSSVR WFEFLHPGQV YRLIAPGPAT PMLFEKDGSS CISRRPLELA GCASCLTVQD NWTLELESSQ DIQDVLDANK SLPESSLTD LLSDNFTDSL VSFSAEILSR TLCEPLVASL WMKLGNTGAM RRCVKLTVAL ETAECEFPPH LDVYIEDPHL P PSLGLLPG ARVHFSQLEK RVSRSHNVYC CFRSSTYVQV LSFPPETTIS IPLPHIYLAE LLQGGQSPFQ ATASCHIVSV FS LQLFWVC AYCTSICRQG KCTRLGSTCP TQTAISQAII RLLVEDGTAE AVVTCRNHHV AAALGLCPRE WASLLDFVQV PGR VVLQFA GPGAQLESSA RVDEPMTMFL WTLCTSPSVL RPIVLSFELE RKPSKIVPLE PPRLQRFQCG ELPFLTHVNP RLRL SCLSI RESEYSSSLG ILASSC

UniProtKB: CST complex subunit CTC1

+
Macromolecule #6: CST complex subunit STN1

MacromoleculeName: CST complex subunit STN1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.172949 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MQPGSSRCEE ETPSLLWGLD PVFLAFAKLY IRDILDMKES RQVPGVFLYN GHPIKQVDVL GTVIGVRERD AFYSYGVDDS TGVINCICW KKLNTESVSA APSAARELSL TSQLKKLQET IEQKTKIEIG DTIRVRGSIR TYREEREIHA TTYYKVDDPV W NIQIARML ...String:
MQPGSSRCEE ETPSLLWGLD PVFLAFAKLY IRDILDMKES RQVPGVFLYN GHPIKQVDVL GTVIGVRERD AFYSYGVDDS TGVINCICW KKLNTESVSA APSAARELSL TSQLKKLQET IEQKTKIEIG DTIRVRGSIR TYREEREIHA TTYYKVDDPV W NIQIARML ELPTIYRKVY DQPFHSSALE KEEALSNPGA LDLPSLTSLL SEKAKEFLME NRVQSFYQQE LEMVESLLSL AN QPVIHSA SSDQVNFKKD TTSKAIHSIF KNAIQLLQEK GLVFQKDDGF DNLYYVTRED KDLHRKIHRI IQQDCQKPNH MEK GCHFLH ILACARLSIR PGLSEAVLQQ VLELLEDQSD IVSTMEHYYT AF

UniProtKB: CST complex subunit STN1

+
Macromolecule #7: CST complex subunit TEN1

MacromoleculeName: CST complex subunit TEN1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.872013 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MMLPKPGTYY LPWEVSAGQV PDGSTLRTFG RLCLYDMIQS RVTLMAQHGS DQHQVLVCTK LVEPFHAQVG SLYIVLGELQ HQQDRGSVV KARVLTCVEG MNLPLLEQAI REQRLYKQER GGSQ

UniProtKB: CST complex subunit TEN1

+
Macromolecule #8: canonical telomeric DNA sequence

MacromoleculeName: canonical telomeric DNA sequence / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.682672 KDa
SequenceString:
(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.075 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was cross-linked with glutaraldehyde (GraFix)

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 131850
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5exr

source_name: PDB, initial_model_type: experimental model

6w6w

source_name: PDB, initial_model_type: experimental model
Output model

PDB-7u5c:
Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more