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Yorodumi- EMDB-18134: Cryo-EM structure of the DNA polymerase holoenzyme E9-A20-D4 of v... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18134 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of the DNA polymerase holoenzyme E9-A20-D4 of vaccinia virus | ||||||||||||||||||||||||
Map data | Sharpened map with b=160 A2, masked. | ||||||||||||||||||||||||
Sample |
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Keywords | DNA polymerase / holoenzyme / processivity factor / uracil-DNA glycosylase / VIRAL PROTEIN | ||||||||||||||||||||||||
Function / homology | Function and homology information uracil-DNA glycosylase / viral DNA genome replication / uracil DNA N-glycosylase activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / nucleotide binding ...uracil-DNA glycosylase / viral DNA genome replication / uracil DNA N-glycosylase activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / nucleotide binding / DNA repair / DNA binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Vaccinia virus / Vaccinia virus Copenhagen | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||||||||||||||
Authors | Burmeister WP / Ballandras-Colas A / Boettcher B / Grimm C | ||||||||||||||||||||||||
Funding support | France, United States, Germany, 7 items
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Citation | Journal: To Be Published Title: Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus Authors: Burmeister WP / Boutin L / Balestra AC / Groeger H / Ballandras-Colas A / Hutin S / Kraft C / Grimm C / Boettcher B / Fischer U / Tarbouriech N / Iseni F | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18134.map.gz | 53 MB | EMDB map data format | |
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Header (meta data) | emd-18134-v30.xml emd-18134.xml | 24.9 KB 24.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18134_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_18134.png | 205.8 KB | ||
Filedesc metadata | emd-18134.cif.gz | 7.8 KB | ||
Others | emd_18134_half_map_1.map.gz emd_18134_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18134 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18134 | HTTPS FTP |
-Related structure data
Related structure data | 8q3rMC 8qamC M: atomic model generated by this map C: citing same article (ref.) |
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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_18134.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map with b=160 A2, masked. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: correct hand, from cryosparc NU refinement
File | emd_18134_half_map_1.map | ||||||||||||
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Annotation | correct hand, from cryosparc NU refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: correct hand, from cryosparc NU refinement
File | emd_18134_half_map_2.map | ||||||||||||
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Annotation | correct hand, from cryosparc NU refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E9-A20-D4 DNA polymerase holoenzyme
Entire | Name: E9-A20-D4 DNA polymerase holoenzyme |
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Components |
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-Supramolecule #1: E9-A20-D4 DNA polymerase holoenzyme
Supramolecule | Name: E9-A20-D4 DNA polymerase holoenzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: heterotrimer |
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Source (natural) | Organism: Vaccinia virus / Strain: Copenhagen |
Molecular weight | Theoretical: 196.825 kDa/nm |
-Macromolecule #1: Uracil-DNA glycosylase
Macromolecule | Name: Uracil-DNA glycosylase / type: protein_or_peptide / ID: 1 / Details: D4 carries a N-terminal Strep-tag / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vaccinia virus Copenhagen |
Molecular weight | Theoretical: 27.468379 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MASWSHPQFE KSGGGGGLVP RGSAMNSVTV SHAPYTITYH DDWEPVMSQL VEFYNEVASW LLRDETSPIP DKFFIQLKQP LRNKRVCVC GIDPYPKDGT GVPFESPNFT KKSIKEIASS ISRLTGVIDY KGYNLNIIDG VIPWNYYLSC KLGETKSHAI Y WDKISKLL ...String: MASWSHPQFE KSGGGGGLVP RGSAMNSVTV SHAPYTITYH DDWEPVMSQL VEFYNEVASW LLRDETSPIP DKFFIQLKQP LRNKRVCVC GIDPYPKDGT GVPFESPNFT KKSIKEIASS ISRLTGVIDY KGYNLNIIDG VIPWNYYLSC KLGETKSHAI Y WDKISKLL LQHITKHVSV LYCLGKTDFS NIRAKLESPV TTIVGYHPAA RDRQFEKDRS FEIINVLLEL DNKAPINWAQ GF IY UniProtKB: Uracil-DNA glycosylase |
-Macromolecule #2: DNA polymerase processivity factor component OPG148
Macromolecule | Name: DNA polymerase processivity factor component OPG148 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vaccinia virus Copenhagen |
Molecular weight | Theoretical: 49.247031 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MTSSADLTNL KELLSLYKSL RFSDSAAIEK YNSLVEWGTS TYWKIGVQKV ANVETSISDY YDEVKNKPFN IDPGYYIFLP VYFGSVFIY SKGKNMVELG SGNSFQIPDD MRSACNKVLD SDNGIDFLRF VLLNNRWIME DAISKYQSPV NIFKLASEYG L NIPKYLEI ...String: MTSSADLTNL KELLSLYKSL RFSDSAAIEK YNSLVEWGTS TYWKIGVQKV ANVETSISDY YDEVKNKPFN IDPGYYIFLP VYFGSVFIY SKGKNMVELG SGNSFQIPDD MRSACNKVLD SDNGIDFLRF VLLNNRWIME DAISKYQSPV NIFKLASEYG L NIPKYLEI EIEEDTLFDD ELYSIIERSF DDKFPKISIS YIKLGELRRQ VVDFFKFSFM YIESIKVDRI GDNIFIPSVI TK SGKKILV KDVDHLIRSK VREHTFVKVK KKNTFSILYD YDGNGTETRG EVIKRIIDTI GRDYYVNGKY FSKVGSAGLK QLT NKLDIN ECATVDELVD EINKSGTVKR KIKNQSAFDL SRECLGYPEA DFITLVNNMR FKIENCKVVN FNIENTNCLN NPSI ETIYR NFNQFVSIFN VVTDVKKRLF E UniProtKB: DNA polymerase processivity factor component OPG148 |
-Macromolecule #3: DNA polymerase
Macromolecule | Name: DNA polymerase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vaccinia virus Copenhagen |
Molecular weight | Theoretical: 120.361484 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMDPDV RCINWFESHG ENRFLYLKSR CRNGETVFIR FPHYFYYVVT DEIYQSLSPP PFNARPLGK MRTIDIDETI SYNLDIKDRK CSVADMWLIE EPKKRSIQNA TMDEFLNISW FYISNGISPD GCYSLDEQYL T KINNGCYH ...String: MSYYHHHHHH DYDIPTTENL YFQGAMDPDV RCINWFESHG ENRFLYLKSR CRNGETVFIR FPHYFYYVVT DEIYQSLSPP PFNARPLGK MRTIDIDETI SYNLDIKDRK CSVADMWLIE EPKKRSIQNA TMDEFLNISW FYISNGISPD GCYSLDEQYL T KINNGCYH CDDPRNCFAK KIPRFDIPRS YLFLDIECHF DKKFPSVFIN PISHTSYCYI DLSGKRLLFT LINEEMLTEQ EI QEAVDRG CLRIQSLMEM DYERELVLCS EIVLLRIAKQ LLELTFDYVV TFNGHNFDLR YITNRLELLT GEKIIFRSPD KKE AVHLCI YERNQSSHKG VGGMANTTFH VNNNNGTIFF DLYSFIQKSE KLDSYKLDSI SKNAFSCMGK VLNRGVREMT FIGD DTTDA KGKAAAFAKV LTTGNYVTVD EDIICKVIRK DIWENGFKVV LLCPTLPNDT YKLSFGKDDV DLAQMYKDYN LNIAL DMAR YCIHDACLCQ YLWEYYGVET KTDAGASTYV LPQSMVFEYR ASTVIKGPLL KLLLETKTIL VRSETKQKFP YEGGKV FAP KQKMFSNNVL IFDYNSLYPN VCIFGNLSPE TLVGVVVSTN RLEEEINNQL LLQKYPPPRY ITVHCEPRLP NLISEIA IF DRSIEGTIPR LLRTFLAERA RYKKMLKQAT SSTEKAIYDS MQYTYKIVAN SVYGLMGFRN SALYSYASAK SCTSIGRR M ILYLESVLNG AELSNGMLRF ANPLSNPFYM DDRDINPIVK TSLPIDYRFR FRSVYGDTDS VFTEIDSQDV DKSIEIAKE LERLINNRVL FNNFKIEFEA VYKNLIMQSK KKYTTMKYSA SSNSKSVPER INKGTSETRR DVSKFHKNMI KTYKTRLSEM LSEGRMNSN QVCIDILRSL ETDLRSEFDS RSSPLELFML SRMHHSNYKS ADNPNMYLVT EYNKNNPETI ELGERYYFAY I CPANVPWT KKLVNIKTYE TIIDRSFKLG SDQRIFYEVY FKRLTSEIVN LLDNKVLCIS FFERMFGSKP TFYEA UniProtKB: DNA polymerase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.6 Component:
Details: 35 mM Tris-HCl, pH 8, 150 mM NaCl, 5 mM EDTA, 3.8 mM desthiobiotin | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.013000000000000001 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 42000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1376 / Average electron dose: 68.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Details | Phenix real-space refinement | ||||||||||||
Refinement | Space: REAL / Protocol: OTHER | ||||||||||||
Output model | PDB-8q3r: |