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- EMDB-29891: Tetramer core subcomplex (conformation 3) of Xenopus laevis DNA p... -
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Open data
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Basic information
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Title | Tetramer core subcomplex (conformation 3) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
![]() | Tetramer core subcomplex (conformation 3) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||
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![]() | Primase / DNA polymerase / chimeric RNA-DNA primer / RNA/DNA hybrid / DNA replication / DNA synthesis / REPLICATION | ||||||||||||
Function / homology | ![]() alpha DNA polymerase:primase complex / DNA primase activity / primosome complex / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication origin binding / DNA replication initiation ...alpha DNA polymerase:primase complex / DNA primase activity / primosome complex / lagging strand elongation / DNA replication, synthesis of primer / mitotic DNA replication initiation / DNA strand elongation involved in DNA replication / leading strand elongation / DNA replication origin binding / DNA replication initiation / nuclear matrix / double-strand break repair via nonhomologous end joining / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin binding / chromatin / nucleolus / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||
![]() | Mullins EA / Chazin WJ / Eichman BF | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α-primase. Authors: Elwood A Mullins / Lauren E Salay / Clarissa L Durie / Noah P Bradley / Jane E Jackman / Melanie D Ohi / Walter J Chazin / Brandt F Eichman Abstract: The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is ...The mechanism by which polymerase α-primase (polα-primase) synthesizes chimeric RNA-DNA primers of defined length and composition, necessary for replication fidelity and genome stability, is unknown. Here, we report cryo-EM structures of polα-primase in complex with primed templates representing various stages of DNA synthesis. Our data show how interaction of the primase regulatory subunit with the primer 5'-end facilitates handoff of the primer to polα and increases polα processivity, thereby regulating both RNA and DNA composition. The structures detail how flexibility within the heterotetramer enables synthesis across two active sites and provide evidence that termination of DNA synthesis is facilitated by reduction of polα and primase affinities for the varied conformations along the chimeric primer/template duplex. Together, these findings elucidate a critical catalytic step in replication initiation and provide a comprehensive model for primer synthesis by polα-primase. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 15.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.5 KB 24.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.6 KB | Display | ![]() |
Images | ![]() | 20.2 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() | 28.4 MB 28.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v5oMC ![]() 8g99C ![]() 8g9fC ![]() 8g9lC ![]() 8g9nC ![]() 8g9oC ![]() 8ucuC ![]() 8ucvC ![]() 8ucwC ![]() 8v5mC ![]() 8v5nC ![]() 8v6gC ![]() 8v6hC ![]() 8v6iC ![]() 8v6jC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Tetramer core subcomplex (conformation 3) of Xenopus laevis DNA polymerase alpha-primase | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.64 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Tetramer core subcomplex (conformation 3) of Xenopus laevis...
File | emd_29891_half_map_1.map | ||||||||||||
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Annotation | Tetramer core subcomplex (conformation 3) of Xenopus laevis DNA polymerase alpha-primase (half 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Tetramer core subcomplex (conformation 3) of Xenopus laevis...
File | emd_29891_half_map_2.map | ||||||||||||
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Annotation | Tetramer core subcomplex (conformation 3) of Xenopus laevis DNA polymerase alpha-primase (half 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Polymerase alpha-primase
Entire | Name: Polymerase alpha-primase |
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Components |
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-Supramolecule #1: Polymerase alpha-primase
Supramolecule | Name: Polymerase alpha-primase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Heterotetrameric protein complex |
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Molecular weight | Theoretical: 300 KDa |
-Supramolecule #2: Polymerase alpha
Supramolecule | Name: Polymerase alpha / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 / Details: Heterodimer consisting of POLA1 and POLA2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 200 KDa |
-Supramolecule #3: Primase
Supramolecule | Name: Primase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 / Details: Heterodimer consisting of PRIM1 and PRIM2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: POLA1
Macromolecule | Name: POLA1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: SNAADGSQVF RFYWLDAYED QYSQPGVVYL FGKVWIESAD AYVSCCVSVK NIERTVYLLP RENRVQLSTG KDTGAPVSMM HVYQEFNEAV AEKYKIMKFK SKKVDKDYAF EIPDVPASSE YLEVRYSADS PQLPQDLKGE TFSHVFGTNT SSLELFLLSR KIKGPSWLEI ...String: SNAADGSQVF RFYWLDAYED QYSQPGVVYL FGKVWIESAD AYVSCCVSVK NIERTVYLLP RENRVQLSTG KDTGAPVSMM HVYQEFNEAV AEKYKIMKFK SKKVDKDYAF EIPDVPASSE YLEVRYSADS PQLPQDLKGE TFSHVFGTNT SSLELFLLSR KIKGPSWLEI KSPQLSSQPM SWCKVEAVVT RPDQVSVVKD LAPPPVVVLS LSMKTVQNAK THQNEIVAIA ALVHHTFPLD KAPPQPPFQT HFCVLSKLND CIFPYDYNEA VKQKNANIEI ALTERTLLGF FLAKIHKIDP DVIVGHDIYG FDLEVLLQRI NSCKVPFWSK IGRLRRSVMP KLGGRSGFAE RNAACGRIIC DIEISAKELI RCKSYHLSEL VHQILKAERV VIPPENIRNA YNDSVHLLYM LENTWIDAKF ILQIMCELNV LPLALQITNI AGNVMSRTLM GGRSERNEYL LLHAFTENNF IVPDKPVFKK MQQTTVEDND DMGTDQNKNK SRKKAAYAGG LVLEPKVGFY DKFILLLDFN SLYPSIIQEY NICFTTVHRE APSTQKGEDQ DEIPELPHSD LEMGILPREI RKLVERRRHV KQLMKQPDLN PDLYLQYDIR QKALKLTANS MYGCLGFSYS RFYAKPLAAL VTHQGREILL HTKEMVQKMN LEVIYGDTDS IMINTNCNNL EEVFKLGNRV KSEINKSYKL LEIDIDGIFK SLLLLKKKKY AALTVEPTGD GKYVTKQELK GLDIVRRDWC ELAKQAGNYV ISQILSDQPR DSIVENIQKK LTEIGENVTN GTVPITQYEI NKALTKDPQD YPDKKSLPHV HVALWINSQG GRKVKAGDTI SYVICQDGSN LSASQRAYAQ EQLQKQENLS IDTQYYLSQQ VHPVVARICE PIDGIDSALI AMWLGLDPSQ FRAHRHYQQD EENDALLGGP SQLTDEEKYR DCERFKFFCP KCGTENIYDN VFDGSGLQIE PGLKRCSKPE CDASPLDYVI QVHNKLLLDI RRYIKKYYSG WLVCEEKTCQ NRTRRLPLSF SRNGPICQAC SKATLRSEYP EKALYTQLCF YRFIFDWDYA LEKVVSEQER GHLKKKLFQE SENQYKKLKS TVDQVLSRSG YSEVNLSKLF QTLNTIK UniProtKB: DNA polymerase alpha catalytic subunit |
-Macromolecule #2: POLA2
Macromolecule | Name: POLA2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: SNAMSVSAKS IAEELKVFDV NFEDEEVPEK MVELCTVHRL KEEDMVNEWM AFSTTRNLPL TVGNLNLLEH EVLNKKSARP RPSLKKEKHC GNRDFNTIQE LIEVETAEEN LLDSYATPAK GSQKRNLSTP EHPQSKRILS INRSPHVLFS PTSFSPSATP SQKYGSRTNR ...String: SNAMSVSAKS IAEELKVFDV NFEDEEVPEK MVELCTVHRL KEEDMVNEWM AFSTTRNLPL TVGNLNLLEH EVLNKKSARP RPSLKKEKHC GNRDFNTIQE LIEVETAEEN LLDSYATPAK GSQKRNLSTP EHPQSKRILS INRSPHVLFS PTSFSPSATP SQKYGSRTNR GEVVTTYGEL QGTTWNGGSG SNTNVELFTS LDEPLTKMYK FMFQKLMDIR EVVSIKIEEL GASLKDHFQI DEFTSVSLPA QETVTVLGQI GCDSNGKLNS KSVILEGDRE HSAGMQVPVD LSELKDYSLF PGQVVIMEGT NSTGRRFVPT KLYEGVPLPF HQPSKEFEEC PQQMVITACG PFTTSDTITY DALKDLIDIV NRDRPDICIL LGPFLDAKHE QIENLQLTVT FEDVFKRCLK MIIEGTRPSG CHLVIVPSLR DVHHDPVYPQ PPFSCFEPAK EDKERVHFVA DPCTLSVNGV VIGMTSTDLL FHMGAEEISS SAGAPDRFSR ILRHILTQRS YYPLYPPNEE INIDYEALYS YTPMPVTPDV FIVPSELRYF IKDVTGCICI NPGRLTKGLV GGTYARFLVK SGAMGSEGKR STCISAQVVR V UniProtKB: DNA polymerase alpha subunit B |
-Macromolecule #3: PRIM2
Macromolecule | Name: PRIM2 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MLFSRDRKYR HNTRLTGDRK GDLYPSSLQF YQHPPTENIS LIEFETFAIE RLKLLKAVEN LGVSYVKNSE EYSKKLELEL RKLKFPYRPL HEEISDDVYD LRRKDHISHF ILRLAYCQSE DLRRWFIQQE MDLFKFRFGL LTKESVQEFL KLNDLQYVAI SEDEKNMHKE ...String: MLFSRDRKYR HNTRLTGDRK GDLYPSSLQF YQHPPTENIS LIEFETFAIE RLKLLKAVEN LGVSYVKNSE EYSKKLELEL RKLKFPYRPL HEEISDDVYD LRRKDHISHF ILRLAYCQSE DLRRWFIQQE MDLFKFRFGL LTKESVQEFL KLNDLQYVAI SEDEKNMHKE DLMNSSFGLS LTKMEDTEFY KVPFQAALDL VRPRKVFLWR GFAFIPHKDI VSIVLNDFRA KLSKALALSA RSLPVVQSDE RLQPLLNHLS HSYIGQDFSS QSNTGKISLE QIDGFAAKSF PLCMRQLHKS LRENHHLRHG GRMQYGLFLK GIGLTLEQAL QFWRLEFTKG KVDSEKFDKV YAYSIRHNYG KEGKRTDYTP YSCMKVILSN PPSQGDYHGC PFRHSDPELL KQKLQSFKVP SSGINQILEL VKGMHYQLAC QKYFELTHSV DDCGFSLNHP NQYFAESQKL LTGSREIKKE QTARDSPAVT ASQLSSSSSS ASIPKSQSSA PEMEDLEQIF SEY UniProtKB: DNA primase large subunit |
-Macromolecule #4: PRIM1
Macromolecule | Name: PRIM1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: GPHMDLSVYD PASLPDVLPL YYRRLFPFYQ YFRWLNYGGV VKNYFQHREF SFTLKDDVYV RYQSFNNQSE LEKEMQKMCP YKIDIGAVYS HRPSLHNTVK SGTFQAQEKE LVFDIDMTDY DDVRRCCSSA DICPKCWTLM TIAVRILDRA LAEDFGFKHR LWVYSGRRGV ...String: GPHMDLSVYD PASLPDVLPL YYRRLFPFYQ YFRWLNYGGV VKNYFQHREF SFTLKDDVYV RYQSFNNQSE LEKEMQKMCP YKIDIGAVYS HRPSLHNTVK SGTFQAQEKE LVFDIDMTDY DDVRRCCSSA DICPKCWTLM TIAVRILDRA LAEDFGFKHR LWVYSGRRGV HCWVCDDSAR KLSQAERSAV AEYLSVVKGG EETIKKVQLP ETIHPFIGKS LKMVERYFEK YALVDQDILE NKQCWDKVIA LVPEVARESL LREFSKARSS VERWDKLSSC LEATGKDFRR YSNIPKEIML QFCYPRLDVN VSKGLNHLLK SPFSVHPKTG RISVPIDCKK LDQFDPFSVP TISLICSELD NVSKKEEDED SAGEGEPEAK KRTRDYKRTS LAPYIKVFEQ FLDKLDQSRK GELLNKSDLK KEF UniProtKB: DNA primase |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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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: 1 / Number real images: 17820 / Average electron dose: 54.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |