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- SASDCM5: Vaccinia virus binary E9 polymerase / DNA complex -

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ID or keywords:

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Basic information

Entry
Database: SASBDB / ID: SASDCM5
SampleVaccinia virus binary E9 polymerase / DNA complex
  • DNA polymerase E9 exo- mutant (protein), E9 exo-, Vaccinia virus (strain Copenhagen)
  • DNA oligomer template-primer hairpin (DNA), DNA hairpinStem-loop, synthetic construct
Function / homology
Function and homology information


viral DNA genome replication / 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 binding
Similarity search - Function
DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / 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-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / 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 / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesVaccinia virus (strain Copenhagen)
synthetic construct (others)
CitationDate: 2017 Dec
Title: The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding
Authors: Tarbouriech N / Ducournau C / Hutin S / Mas P / Man P / Forest E / Hart D / Peyrefitte C / Burmeister W
Contact author
  • Wim Burmeister (IBS, Institut de Biologie Structurale, Grenoble, France)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #1359
Type: atomic / Radius of dummy atoms: 1.90 A / Symmetry: none
Comment: DNA and conformation from entry 3iay, domainwise alignment of E9 structure
Chi-square value: 1.083 / P-value: 0.000120
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Vaccinia virus binary E9 polymerase / DNA complex / Entity id: 726 / 727
BufferName: 20 mM Tris HCl, 100 mM NaCl, 4 mM DTT / pH: 7
Entity #726Name: E9 exo- / Type: protein / Description: DNA polymerase E9 exo- mutant / Formula weight: 117.14 / Num. of mol.: 1 / Source: Vaccinia virus (strain Copenhagen) / References: UniProt: P20509
Sequence: GAMDPDVRCI NWFESHGENR FLYLKSRCRN GETVFIRFPH YFYYVVTDEI YQSLSPPPFN ARPLGKMRTI DIDETISYNL DIKDRKCSVA DMWLIEEPKK RSIQNATMDE FLNISWFYIS NGISPDGCYS LDEQYLTKIN NGCYHCDDPR NCFAKKIPRF DIPRSYLFLA ...Sequence:
GAMDPDVRCI NWFESHGENR FLYLKSRCRN GETVFIRFPH YFYYVVTDEI YQSLSPPPFN ARPLGKMRTI DIDETISYNL DIKDRKCSVA DMWLIEEPKK RSIQNATMDE FLNISWFYIS NGISPDGCYS LDEQYLTKIN NGCYHCDDPR NCFAKKIPRF DIPRSYLFLA IACHFDKKFP SVFINPISHT SYCYIDLSGK RLLFTLINEE MLTEQEIQEA VDRGCLRIQS LMEMDYEREL VLCSEIVLLR IAKQLLELTF DYVVTFNGHN FDLRYITNRL ELLTGEKIIF RSPDKKEAVH LCIYERNQSS HKGVGGMANT TFHVNNNNGT IFFDLYSFIQ KSEKLDSYKL DSISKNAFSC MGKVLNRGVR EMTFIGDDTT DAKGKAAAFA KVLTTGNYVT VDEDIICKVI RKDIWENGFK VVLLCPTLPN DTYKLSFGKD DVDLAQMYKD YNLNIALDMA RYCIHDACLC QYLWEYYGVE TKTDAGASTY VLPQSMVFEY RASTVIKGPL LKLLLETKTI LVRSETKQKF PYEGGKVFAP KQKMFSNNVL IFDYNSLYPN VCIFGNLSPE TLVGVVVSTN RLEEEINNQL LLQKYPPPRY ITVHCEPRLP NLISEIAIFD RSIEGTIPRL LRTFLAERAR YKKMLKQATS STEKAIYDSM QYTYKIVANS VYGLMGFRNS ALYSYASAKS CTSIGRRMIL YLESVLNGAE LSNGMLRFAN PLSNPFYMDD RDINPIVKTS LPIDYRFRFR SVYGDTDSVF TEIDSQDVDK SIEIAKELER LINNRVLFNN FKIEFEAVYK NLIMQSKKKY TTMKYSASSN SKSVPERINK GTSETRRDVS KFHKNMIKTY KTRLSEMLSE GRMNSNQVCI DILRSLETDL RSEFDSRSSP LELFMLSRMH HSNYKSADNP NMYLVTEYNK NNPETIELGE RYYFAYICPA NVPWTKKLVN IKTYETIIDR SFKLGSDQRI FYEVYFKRLT SEIVNLLDNK VLCISFFERM FGSKPTFYEA
Entity #727Name: DNA hairpinStem-loop / Type: DNA / Description: DNA oligomer template-primer hairpin / Formula weight: 9.014 / Num. of mol.: 1 / Source: synthetic construct
Sequence:
AAAGGCGCTG CTGAGTTTTC TCAGCAGCG

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Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.0992 Å / Dist. spec. to detc.: 2.864 mm
DetectorName: Pilatus 1M
Scan
Title: Binary E9 polymerase / DNA complex / Measurement date: Mar 12, 2015 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 700 / Unit: 1/nm /
MinMax
Q0.0432 4.9752
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 259 /
MinMax
Q0.04555 2.493
P(R) point1 259
R0 12
Result
Type of curve: other /
ExperimentalPorod
MW127 kDa127 kDa
Volume-210 nm3

P(R)GuinierGuinier error
Forward scattering, I087.79 87.94 0.13
Radius of gyration, Rg3.45 nm3.47 nm0.02

MinMax
D-12
Guinier point13 66

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