[English] 日本語
Yorodumi- EMDB-27109: Human CST-DNA polymerase alpha/primase preinitiation complex boun... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27109 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human CST-DNA polymerase alpha/primase preinitiation complex bound to 6xTEL DNA template | |||||||||
Map data | Merged map from three separately local refined domains as described in the manuscript. | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 Å | |||||||||
Authors | He Q / Lin X / Chavez BL / Agrawal S / Lusk BL / Lim C | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Nature / Year: 2022 Title: Structures of the human CST-Polα-primase complex bound to telomere templates. Authors: Qixiang He / Xiuhua Lin / Bianca L Chavez / Sourav Agrawal / Benjamin L Lusk / Ci Ji Lim / Abstract: The mammalian DNA polymerase-α-primase (Polα-primase) complex is essential for DNA metabolism, providing the de novo RNA-DNA primer for several DNA replication pathways such as lagging-strand ...The mammalian DNA polymerase-α-primase (Polα-primase) complex is essential for DNA metabolism, providing the de novo RNA-DNA primer for several DNA replication pathways such as lagging-strand synthesis and telomere C-strand fill-in. The physical mechanism underlying how Polα-primase, alone or in partnership with accessory proteins, performs its complicated multistep primer synthesis function is unknown. Here we show that CST, a single-stranded DNA-binding accessory protein complex for Polα-primase, physically organizes the enzyme for efficient primer synthesis. Cryogenic electron microscopy structures of the CST-Polα-primase preinitiation complex (PIC) bound to various types of telomere overhang reveal that template-bound CST partitions the DNA and RNA catalytic centres of Polα-primase into two separate domains and effectively arranges them in RNA-DNA synthesis order. The architecture of the PIC provides a single solution for the multiple structural requirements for the synthesis of RNA-DNA primers by Polα-primase. Several insights into the template-binding specificity of CST, template requirement for assembly of the CST-Polα-primase PIC and activation are also revealed in this study. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27109.map.gz | 6.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27109-v30.xml emd-27109.xml | 29.9 KB 29.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27109_fsc.xml | 18.3 KB | Display | FSC data file |
Images | emd_27109.png | 66.9 KB | ||
Others | emd_27109_additional_1.map.gz emd_27109_additional_2.map.gz emd_27109_half_map_1.map.gz emd_27109_half_map_2.map.gz | 122.5 MB 230.5 MB 226.4 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27109 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27109 | HTTPS FTP |
-Validation report
Summary document | emd_27109_validation.pdf.gz | 698.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_27109_full_validation.pdf.gz | 698.5 KB | Display | |
Data in XML | emd_27109_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_27109_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27109 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27109 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_27109.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Merged map from three separately local refined domains as described in the manuscript. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Unsharpened consensus map
File | emd_27109_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened consensus map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened consensus map
File | emd_27109_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened consensus map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A
File | emd_27109_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map B
File | emd_27109_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human CST-DNA polymerase alpha/primase preinitiation complex boun...
Entire | Name: Human CST-DNA polymerase alpha/primase preinitiation complex bound to 6xTEL DNA template |
---|---|
Components |
|
-Supramolecule #1: Human CST-DNA polymerase alpha/primase preinitiation complex boun...
Supramolecule | Name: Human CST-DNA polymerase alpha/primase preinitiation complex bound to 6xTEL DNA template type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 540 KDa |
-Macromolecule #1: CTC1
Macromolecule | Name: CTC1 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGDYKDHDGD YKDHDIDYKD DDDKSGGSLE AAGRAQVPSS EQAWLEDAQV FIQKTLCPAV KEPNVQLTPL VIDCVKTVWL SQGRNQGSTL PLSYSFVSVQ DLKTHQRLPC CSHLSWSSSA YQAWAQEAGP NGNPLPREQL LLLGTLTDLS ADLEQECRNG SLYVRDNTGV ...String: MGDYKDHDGD YKDHDIDYKD DDDKSGGSLE AAGRAQVPSS EQAWLEDAQV FIQKTLCPAV KEPNVQLTPL VIDCVKTVWL SQGRNQGSTL PLSYSFVSVQ DLKTHQRLPC CSHLSWSSSA YQAWAQEAGP NGNPLPREQL LLLGTLTDLS ADLEQECRNG SLYVRDNTGV LSCELIDLDL SWLGHLFLFP RWSYLPPARW NSSGEGHLEL WDAPVPVFPL TISPGPVTPI PVLYPESASC LLRLRNKLRG VQRNLAGSLV RLSALVKSKQ KAYFILSLGR SHPAVTHVSI IVQVPAQLVW HRALRPGTAY VLTELRVSKI RGQRQHVWMT SQSSRLLLLK PECVQELELE LEGPLLEADP KPLPMPSNSE DKKDPESLVR YSRLLSYSGA VTGVLNEPAG LYELDGQLGL CLAYQQFRGL RRVMRPGVCL QLQDVHLLQS VGGGTRRPVL APCLRGAVLL QSFSRQKPGA HSSRQAYGAS LYEQLVWERQ LGLPLYLWAT KALEELACKL CPHVLRHHQF LQHSSPGSPS LGLQLLAPTL DLLAPPGSPV RNAHNEILEE PHHCPLQKYT RLQTPSSFPT LATLKEEGQR KAWASFDPKA LLPLPEASYL PSCQLNRRLA WSWLCLLPSA FCPAQVLLGV LVASSHKGCL QLRDQSGSLP CLLLAKHSQP LSDPRLIGCL VRAERFQLIV ERDVRSSFPS WKELSMPGFI QKQQARVYVQ FFLADALILP VPRPCLHSAT PSTPQTDPTG PEGPHLGQSR LFLLCHKEAL MKRNFCVPPG ASPEVPKPAL SFYVLGSWLG GTQRKEGTGW GLPEPQGNDD NDQKVHLIFF GSSVRWFEFL HPGQVYRLVA PGPATPMLFE KDGSSCISRR PLELAGCASC LTVQDNWTLE LESSQDIQDV LDANKSLPES SLTDLLSDNF TDSLVSFSAE ILSRTLCEPL VASLWMKLGN TGAMRRCVKL TVALETAECE FPPHLDVYIE DPHLPPSLGL LPGARVHFSQ LEKRVSRSHN VYCCFRSSTY VQVLSFPPET TISVPLPHIY LAELLQGGQS PFQATASCHI VSVFSLQLFW VCAYCTSICR QGKCTRLGST CPTQTAISQA IIRLLVEDGT AEAVVTCRNH HVAAALGLCP REWASLLDFV QVPGRVVLQF AGPGAQLESS ARVDEPMTMF LWTLCTSPSV LRPIVLSFEL ERKPSKIVPL EPPRLQRFQC GELPFLTHVN PRLRLSCLSI RESEYSSSLG ILASSC |
-Macromolecule #2: STN1
Macromolecule | Name: STN1 / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MHHHHHHQPG SSRCEEETPS LLWGLDPVFL AFAKLYIRDI LDMKESRQVP GVFLYNGHPI KQVDVLGTVI GVRERDAFYS YGVDDSTGVI NCICWKKLNT ESVSAAPSAA RELSLTSQLK KLQETIEQKT KIEIGDTIRV RGSIRTYREE REIHATTYYK VDDPVWNIQI ...String: MHHHHHHQPG SSRCEEETPS LLWGLDPVFL AFAKLYIRDI LDMKESRQVP GVFLYNGHPI KQVDVLGTVI GVRERDAFYS YGVDDSTGVI NCICWKKLNT ESVSAAPSAA RELSLTSQLK KLQETIEQKT KIEIGDTIRV RGSIRTYREE REIHATTYYK VDDPVWNIQI ARMLELPTIY RKVYDQPFHS SALEKEEALS NPGALDLPSL TSLLSEKAKE FLMENRVQSF YQQELEMVES LLSLANQPVI HSASSDQVNF KKDTTSKAIH SIFKNAIQLL QEKGLVFQKD DGFDNLYYVT REDKDLHRKI HRIIQQDCQK PNHMEKGCHF LHILACARLS IRPGLSEAVL QQVLELLEDQ SDIVSTMEHY YTAF |
-Macromolecule #3: TEN1
Macromolecule | Name: TEN1 / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMGSGI QLPKPGTYYL PWEVSAGQVP DGSTLRTFGR LCLYDMIQSR VTLMAQHGSD QHQVLVCTKL VEPFHAQVGS LYIVLGELQH QQDRGSVVKA RVLTCVEGMN LPLLEQAIRE QRLYKQERGG SQ |
-Macromolecule #4: PRIM1
Macromolecule | Name: PRIM1 / type: protein_or_peptide / ID: 4 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGHHHHHHGS GSGSGETFDP TELPELLKLY YRRLFPYSQY YRWLNYGGVI KNYFQHREFS FTLKDDIYIR YQSFNNQSDL EKEMQKMNPY KIDIGAVYSH RPNQHNTVKL GAFQAQEKEL VFDIDMTDYD DVRRCCSSAD ICPKCWTLMT MAIRIIDRAL KEDFGFKHRL ...String: MGHHHHHHGS GSGSGETFDP TELPELLKLY YRRLFPYSQY YRWLNYGGVI KNYFQHREFS FTLKDDIYIR YQSFNNQSDL EKEMQKMNPY KIDIGAVYSH RPNQHNTVKL GAFQAQEKEL VFDIDMTDYD DVRRCCSSAD ICPKCWTLMT MAIRIIDRAL KEDFGFKHRL WVYSGRRGVH CWVCDESVRK LSSAVRSGIV EYLSLVKGGQ DVKKKVHLSE KIHPFIRKSI NIIKKYFEEY ALVNQDILEN KESWDKILAL VPETIHDELQ QSFQKSHNSL QRWEHLKKVA SRYQNNIKND KYGPWLEWEI MLQYCFPRLD INVSKGINHL LKSPFSVHPK TGRISVPIDL QKVDQFDPFT VPTISFICRE LDAISTNEEE KEENEAESDV KHRTRDYKKT SLAPYVKVFE HFLENLDKSR KGELLKKSDL QKDF |
-Macromolecule #5: PRIM2
Macromolecule | Name: PRIM2 / type: protein_or_peptide / ID: 5 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGHHHHHHGS GSGSGEFSGR KWRKLRLAGD QRNASYPHCL QFYLQPPSEN ISLIEFENLA IDRVKLLKSV ENLGVSYVKG TEQYQSKLES ELRKLKFSYR ENLEDEYEPR RRDHISHFIL RLAYCQSEEL RRWFIQQEMD LLRFRFSILP KDKIQDFLKD SQLQFEAISD ...String: MGHHHHHHGS GSGSGEFSGR KWRKLRLAGD QRNASYPHCL QFYLQPPSEN ISLIEFENLA IDRVKLLKSV ENLGVSYVKG TEQYQSKLES ELRKLKFSYR ENLEDEYEPR RRDHISHFIL RLAYCQSEEL RRWFIQQEMD LLRFRFSILP KDKIQDFLKD SQLQFEAISD EEKTLREQEI VASSPSLSGL KLGFESIYKI PFADALDLFR GRKVYLEDGF AYVPLKDIVA IILNEFRAKL SKALALTARS LPAVQSDERL QPLLNHLSHS YTGQDYSTQG NVGKISLDQI DLLSTKSFPP CMRQLHKALR ENHHLRHGGR MQYGLFLKGI GLTLEQALQF WKQEFIKGKM DPDKFDKGYS YNIRHSFGKE GKRTDYTPFS CLKIILSNPP SQGDYHGCPF RHSDPELLKQ KLQSYKISPG GISQILDLVK GTHYQVACQK YFEMIHNVDD CGFSLNHPNQ FFCESQRILN GGKDIKKEPI QPETPQPKPS VQKTKDASSA LASLNSSLEM DMEGLEDYFS EDS |
-Macromolecule #6: POLA1
Macromolecule | Name: POLA1 / type: protein_or_peptide / ID: 6 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGGSAGDYKD HDGDYKDHDI DYKDDDDKGA SSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGAGSAPVHG DDSLSDSGSF VSSRARREKK SKKGRQEALE RLKKAKAGEK YKYEVEDFTG VYEEVDEEQY SKLVQARQDD DWIVDDDGIG YVEDGREIFD DDLEDDALDA ...String: MGGSAGDYKD HDGDYKDHDI DYKDDDDKGA SSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGAGSAPVHG DDSLSDSGSF VSSRARREKK SKKGRQEALE RLKKAKAGEK YKYEVEDFTG VYEEVDEEQY SKLVQARQDD DWIVDDDGIG YVEDGREIFD DDLEDDALDA DEKGKDGKAR NKDKRNVKKL AVTKPNNIKS MFIACAGKKT ADKAVDLSKD GLLGDILQDL NTETPQITPP PVMILKKKRS IGASPNPFSV HTATAVPSGK IASPVSRKEP PLTPVPLKRA EFAGDDVQVE STEEEQESGA MEFEDGDFDE PMEVEEVDLE PMAAKAWDKE SEPAEEVKQE ADSGKGTVSY LGSFLPDVSC WDIDQEGDSS FSVQEVQVDS SHLPLVKGAD EEQVFHFYWL DAYEDQYNQP GVVFLFGKVW IESAETHVSC CVMVKNIERT LYFLPREMKI DLNTGKETGT PISMKDVYEE FDEKIATKYK IMKFKSKPVE KNYAFEIPDV PEKSEYLEVK YSAEMPQLPQ DLKGETFSHV FGTNTSSLEL FLMNRKIKGP CWLEVKSPQL LNQPVSWCKV EAMALKPDLV NVIKDVSPPP LVVMAFSMKT MQNAKNHQNE IIAMAALVHH SFALDKAAPK PPFQSHFCVV SKPKDCIFPY AFKEVIEKKN VKVEVAATER TLLGFFLAKV HKIDPDIIVG HNIYGFELEV LLQRINVCKA PHWSKIGRLK RSNMPKLGGR SGFGERNATC GRMICDVEIS AKELIRCKSY HLSELVQQIL KTERVVIPME NIQNMYSESS QLLYLLEHTW KDAKFILQIM CELNVLPLAL QITNIAGNIM SRTLMGGRSE RNEFLLLHAF YENNYIVPDK QIFRKPQQKL GDEDEEIDGD TNKYKKGRKK AAYAGGLVLD PKVGFYDKFI LLLDFNSLYP SIIQEFNICF TTVQRVASEA QKVTEDGEQE QIPELPDPSL EMGILPREIR KLVERRKQVK QLMKQQDLNP DLILQYDIRQ KALKLTANSM YGCLGFSYSR FYAKPLAALV TYKGREILMH TKEMVQKMNL EVIYGDTDSI MINTNSTNLE EVFKLGNKVK SEVNKLYKLL EIDIDGVFKS LLLLKKKKYA ALVVEPTSDG NYVTKQELKG LDIVRRDWCD LAKDTGNFVI GQILSDQSRD TIVENIQKRL IEIGENVLNG SVPVSQFEIN KALTKDPQDY PDKKSLPHVH VALWINSQGG RKVKAGDTVS YVICQDGSNL TASQRAYAPE QLQKQDNLTI DTQYYLAQQI HPVVARICEP IDGIDAVLIA TWLGLDPTQF RVHHYHKDEE NDALLGGPAQ LTDEEKYRDC ERFKCPCPTC GTENIYDNVF DGSGTDMEPS LYRCSNIDCK ASPLTFTVQL SNKLIMDIRR FIKKYYDGWL ICEEPTCRNR TRHLPLQFSR TGPLCPACMK ATLQPEYSDK SLYTQLCFYR YIFDAECALE KLTTDHEKDK LKKQFFTPKV LQDYRKLKNT AEQFLSRSGY SEVNLSKLFA GCAVKSV |
-Macromolecule #7: POLA2
Macromolecule | Name: POLA2 / type: protein_or_peptide / ID: 7 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGHHHHHHGS GSGSGSASAQ QLAEELQIFG LDCEEALIEK LVELCVQYGQ NEEGMVGELI AFCTSTHKVG LTSEILNSFE HEFLSKRLSK ARHSTCKDSG HAGARDIVSI QELIEVEEEE EILLNSYTTP SKGSQKRAIS TPETPLTKRS VSTRSPHQLL SPSSFSPSAT ...String: MGHHHHHHGS GSGSGSASAQ QLAEELQIFG LDCEEALIEK LVELCVQYGQ NEEGMVGELI AFCTSTHKVG LTSEILNSFE HEFLSKRLSK ARHSTCKDSG HAGARDIVSI QELIEVEEEE EILLNSYTTP SKGSQKRAIS TPETPLTKRS VSTRSPHQLL SPSSFSPSAT PSQKYNSRSN RGEVVTSFGL AQGVSWSGRG GAGNISLKVL GCPEALTGSY KSMFQKLPDI REVLTCKIEE LGSELKEHYK IEAFTPLLAP AQEPVTLLGQ IGCDSNGKLN NKSVILEGDR EHSSGAQIPV DLSELKEYSL FPGQVVIMEG INTTGRKLVA TKLYEGVPLP FYQPTEEDAD FEQSMVLVAC GPYTTSDSIT YDPLLDLIAV INHDRPDVCI LFGPFLDAKH EQVENCLLTS PFEDIFKQCL RTIIEGTRSS GSHLVFVPSL RDVHHEPVYP QPPFSYSDLS REDKKQVQFV SEPCSLSING VIFGLTSTDL LFHLGAEEIS SSSGTSDRFS RILKHILTQR SYYPLYPPQE DMAIDYESFY VYAQLPVTPD VLIIPSELRY FVKDVLGCVC VNPGRLTKGQ VGGTFARLYL RRPAADGAER QSPCIAVQVV RI |
-Macromolecule #8: C-6xTEL
Macromolecule | Name: C-6xTEL / type: protein_or_peptide / ID: 8 / Enantiomer: DEXTRO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: CTTAGGGTTA GGGTTAGGGT TAGGGTTAGG GTTAGGG |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
Details: CHAPSO is only added just before sample vitrification. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7794 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |