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Yorodumi- EMDB-27256: Human DNA polymerase alpha/primase elongation complex I bound to ... -
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-Basic information
Entry | Database: EMDB / ID: EMD-27256 | |||||||||
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Title | Human DNA polymerase alpha/primase elongation complex I bound to primer/template | |||||||||
Map data | Unsharpened and flipped and resampled map | |||||||||
Sample |
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Keywords | DNA replication / human DNA polymerase alpha/primase / human primosome / elongation complex / REPLICATION | |||||||||
Function / homology | Function and homology information positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / Polymerase switching / alpha DNA polymerase:primase complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate ...positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / Polymerase switching / alpha DNA polymerase:primase complex / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / primosome complex / DNA replication, synthesis of primer / lagging strand elongation / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / G1/S-Specific Transcription / leading strand elongation / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / double-strand break repair via nonhomologous end joining / nuclear matrix / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleotide binding / chromatin binding / chromatin / nucleolus / protein kinase binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | He Q / Baranovskiy A / Lim C / Tahirov T | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structures of human primosome elongation complexes. Authors: Qixiang He / Andrey G Baranovskiy / Lucia M Morstadt / Alisa E Lisova / Nigar D Babayeva / Benjamin L Lusk / Ci Ji Lim / Tahir H Tahirov / Abstract: The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. ...The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27256.map.gz | 30.3 MB | EMDB map data format | |
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Header (meta data) | emd-27256-v30.xml emd-27256.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27256_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_27256.png | 96 KB | ||
Filedesc metadata | emd-27256.cif.gz | 7.8 KB | ||
Others | emd_27256_half_map_1.map.gz emd_27256_half_map_2.map.gz | 48.8 MB 48.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27256 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27256 | HTTPS FTP |
-Validation report
Summary document | emd_27256_validation.pdf.gz | 723.2 KB | Display | EMDB validaton report |
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Full document | emd_27256_full_validation.pdf.gz | 722.7 KB | Display | |
Data in XML | emd_27256_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_27256_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27256 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27256 | HTTPS FTP |
-Related structure data
Related structure data | 8d96MC 8d9dC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27256.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Unsharpened and flipped and resampled map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B
File | emd_27256_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_27256_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Elongation complex I of human DNA polymerase alpha/primase bound ...
Entire | Name: Elongation complex I of human DNA polymerase alpha/primase bound to RNA-DNA primer and DNA template |
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Components |
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-Supramolecule #1: Elongation complex I of human DNA polymerase alpha/primase bound ...
Supramolecule | Name: Elongation complex I of human DNA polymerase alpha/primase bound to RNA-DNA primer and DNA template type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Smaller elongation complex solved using cryo-EM single-particle analysis |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 340 KDa |
-Macromolecule #1: DNA primase large subunit
Macromolecule | Name: DNA primase large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 58.890918 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENL EDEYEPRRRD HISHFILRLA YCQSEELRRW FIQQEMDLLR FRFSILPKDK IQDFLKDSQL QFEAISDEEK T LREQEIVA ...String: MEFSGRKWRK LRLAGDQRNA SYPHCLQFYL QPPSENISLI EFENLAIDRV KLLKSVENLG VSYVKGTEQY QSKLESELRK LKFSYRENL EDEYEPRRRD HISHFILRLA YCQSEELRRW FIQQEMDLLR FRFSILPKDK IQDFLKDSQL QFEAISDEEK T LREQEIVA SSPSLSGLKL GFESIYKIPF ADALDLFRGR KVYLEDGFAY VPLKDIVAII LNEFRAKLSK ALALTARSLP AV QSDERLQ PLLNHLSHSY TGQDYSTQGN VGKISLDQID LLSTKSFPPC MRQLHKALRE NHHLRHGGRM QYGLFLKGIG LTL EQALQF WKQEFIKGKM DPDKFDKGYS YNIRHSFGKE GKRTDYTPFS CLKIILSNPP SQGDYHGCPF RHSDPELLKQ KLQS YKISP GGISQILDLV KGTHYQVACQ KYFEMIHNVD DCGFSLNHPN QFFCESQRIL NGGKDIKKEP IQPETPQPKP SVQKT KDAS SALASLNSSL EMDMEGLEDY FSEDS UniProtKB: DNA primase large subunit |
-Macromolecule #2: DNA polymerase alpha catalytic subunit
Macromolecule | Name: DNA polymerase alpha catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 166.131094 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MAPVHGDDSL SDSGSFVSSR ARREKKSKKG RQEALERLKK AKAGEKYKYE VEDFTGVYEE VDEEQYSKLV QARQDDDWIV DDDGIGYVE DGREIFDDDL EDDALDADEK GKDGKARNKD KRNVKKLAVT KPNNIKSMFI ACAGKKTADK AVDLSKDGLL G DILQDLNT ...String: MAPVHGDDSL SDSGSFVSSR ARREKKSKKG RQEALERLKK AKAGEKYKYE VEDFTGVYEE VDEEQYSKLV QARQDDDWIV DDDGIGYVE DGREIFDDDL EDDALDADEK GKDGKARNKD KRNVKKLAVT KPNNIKSMFI ACAGKKTADK AVDLSKDGLL G DILQDLNT ETPQITPPPV MILKKKRSIG ASPNPFSVHT ATAVPSGKIA SPVSRKEPPL TPVPLKRAEF AGDDVQVEST EE EQESGAM EFEDGDFDEP MEVEEVDLEP MAAKAWDKES EPAEEVKQEA DSGKGTVSYL GSFLPDVSCW DIDQEGDSSF SVQ EVQVDS SHLPLVKGAD EEQVFHFYWL DAYEDQYNQP GVVFLFGKVW IESAETHVSC CVMVKNIERT LYFLPREMKI DLNT GKETG TPISMKDVYE EFDEKIATKY KIMKFKSKPV EKNYAFEIPD VPEKSEYLEV KYSAEMPQLP QDLKGETFSH VFGTN TSSL ELFLMNRKIK GPCWLEVKSP QLLNQPVSWC KVEAMALKPD LVNVIKDVSP PPLVVMAFSM KTMQNAKNHQ NEIIAM AAL VHHSFALDKA APKPPFQSHF CVVSKPKDCI FPYAFKEVIE KKNVKVEVAA TERTLLGFFL AKVHKIDPDI IVGHNIY GF ELEVLLQRIN VCKAPHWSKI GRLKRSNMPK LGGRSGFGER NATCGRMICD VEISAKELIR CKSYHLSELV QQILKTER V VIPMENIQNM YSESSQLLYL LEHTWKDAKF ILQIMCELNV LPLALQITNI AGNIMSRTLM GGRSERNEFL LLHAFYENN YIVPDKQIFR KPQQKLGDED EEIDGDTNKY KKGRKKAAYA GGLVLDPKVG FYDKFILLLD FNSLYPSIIQ EFNICFTTVQ RVASEAQKV TEDGEQEQIP ELPDPSLEMG ILPREIRKLV ERRKQVKQLM KQQDLNPDLI LQYDIRQKAL KLTANSMYGC L GFSYSRFY AKPLAALVTY KGREILMHTK EMVQKMNLEV IYGDTDSIMI NTNSTNLEEV FKLGNKVKSE VNKLYKLLEI DI DGVFKSL LLLKKKKYAA LVVEPTSDGN YVTKQELKGL DIVRRDWCDL AKDTGNFVIG QILSDQSRDT IVENIQKRLI EIG ENVLNG SVPVSQFEIN KALTKDPQDY PDKKSLPHVH VALWINSQGG RKVKAGDTVS YVICQDGSNL TASQRAYAPE QLQK QDNLT IDTQYYLAQQ IHPVVARICE PIDGIDAVLI ATWLGLDPTQ FRVHHYHKDE ENDALLGGPA QLTDEEKYRD CERFK CPCP TCGTENIYDN VFDGSGTDME PSLYRCSNID CKASPLTFTV QLSNKLIMDI RRFIKKYYDG WLICEEPTCR NRTRHL PLQ FSRTGPLCPA CMKATLQPEY SDKSLYTQLC FYRYIFDAEC ALEKLTTDHE KDKLKKQFFT PKVLQDYRKL KNTAEQF LS RSGYSEVNLS KLFAGCAVKS UniProtKB: DNA polymerase alpha catalytic subunit |
-Macromolecule #3: DNA/RNA (5'-GTP)-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3')
Macromolecule | Name: DNA/RNA (5'-GTP)-R(P*GP*CP*GP*GP*CP*AP*CP*G)-D(P*AP*CP*C)-3') type: other / ID: 3 / Number of copies: 1 Classification: polydeoxyribonucleotide/polyribonucleotide hybrid |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.977352 KDa |
Sequence | String: (GTP)GCGGCACG(DA) (DC)(DC) |
-Macromolecule #4: DNA (5'-D(*AP*TP*AP*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*...
Macromolecule | Name: DNA (5'-D(*AP*TP*AP*AP*TP*GP*GP*TP*CP*GP*TP*GP*CP*CP*GP*CP*CP*AP*AP*TP*AP*A)-3') type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 6.760392 KDa |
Sequence | String: (DA)(DT)(DA)(DA)(DT)(DG)(DG)(DT)(DC)(DG) (DT)(DG)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DT) (DA)(DA) |
-Macromolecule #5: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Macromolecule | Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: DTP |
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Molecular weight | Theoretical: 491.182 Da |
Chemical component information | ChemComp-DTP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: CHAPSO is made fresh at 80 mM before added to the sample at a final concentration of 4-8 mM immediately before vitrification. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 13243 / 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |