REL PDBe PDBe PDBe 2011-04-06 2012-02-17 2012-02-17 2012-02-17 EcoR124 Type I DNA restriction-modification enzyme complex (in closed state) with bound DNA mimic protein Ocr from phage T7. 3D reconstruction by single particle analysis from negative stain EM. Kennaway CK Taylor JE Song CF Potrzebowski W White JH Swiderska A Obarska-Kosinska A Callow P Cooper LP Roberts GA Bujnicki JM Trinick J Kneale GG Dryden DTF EcoR124, endonuclease, methyltransferase, type I restriction, DNA mimic, HsdS, HsdM, HsdR, electron microscopy, negative stain, translocase, DEAD-box, ATPase, antirestriction, phage, T7 Kennaway CK Taylor JE Song CF Potrzebowski W Nicholson W White JH Swiderska A Obarska-Kosinska A Callow P Cooper LP Roberts GA Artero JB Bujnicki JM Trinick J Kneale GG Dryden DT Structure and operation of the DNA-translocating type I DNA restriction enzymes. GENES DEV. 26 92 104 2012 22215814 doi:10.1101/gad.179085.111 EcoR124I R2 M2 S1 complex with dimeric Ocr bound at target recognition domains EcoR124I R2 M2 S1 complex with dimeric Ocr bound at target recognition domains
Stained with uranyl acetate
1x HsdS, 2x HsdM, 2x HsdR, 2x Ocr 4 0.428 EcoR124I HsdS specificity subunit Escherichia coli R Cytoplasmic 0.05 1 Monomer false GO:0005515 IPR000055 EcoR124I HsdM methyltransferase subunit Escherichia coli R cytoplasm 0.059 2 Dimer false GO:0005515 IPR003356 EcoR124I HsdR endonuclease subunit Escherichia coli R 0.12 2 Monomer false GO:0009307 IPR004473 ORF 0.3 Ocr antirestriction protein Enterobacteria phage T7 T7 0.027
Ocr forms a dimer that mimics B-form DNA in shape and charge distrubution.
2 Dimer true Escherichia coli IPR014798 singleParticle particle 0.050 4.7
20mM Tris-Cl, 100 mM NaCl
 NEGATIVE
Protein was adsorbed onto UV treated carbon for 1 minute, blotted, then 1% uranyl acetate solution was applied for 1 min then blotted, three times.
400 mesh copper, continuous carbon
 NONE OTHER
Negative stain
 JEOL 1200EXII FLOOD BEAM BRIGHT FIELD TUNGSTEN HAIRPIN 80 2.0 0.391 1.357 40000.0 37833.0 JEOL 294 Corrected at 80,000x
Customised JEOL 1200 EX microscope, low dose mode.
2011-01-13 KODAK SO-163 FILM OTHER 15 7 40
Scanned on Imacon scanner
8. Side entry
1.5 Ocr (dimer) to EcoR124 molar ratio. The particles were manually selected using boxer. Smaller R1 complexes were removed by alignment and MSA classification.
Filtered at 1st zero
 C2 OTHER 24.0 FSC 0.5 CUT-OFF EMAN, IMAGIC
Refined in Imagic using anchor set. C2 symmetry imposed.
748
Euler angle range limited to plus minus 30 degrees from single axis of rotation
 48 emd_1892.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 80 80 80 -40 -40 -40 80 80 80 316.8 316.8 316.8 90.0 90.0 90.0 X Y Z -5.1513052 9.923256869999999 -0.00000001 1.0 3.96 3.96 3.96 3.2 AUTHOR 3D reconstruction of EcoR124I Type I restriction enzyme complex with a bound antirestriction protein Ocr.
::::EMDATABANK.org::::EMD-1892::::
 2W00 A RIGID BODY FIT Chimera
PDBEntryID_givenInChain. Protocol: rigid body. HsdR (2W00) was fitted into the density after the core methylase (HsdS and 2x HsdM) was fitted. Ocr docked into DNA binding sites (target recognition domains) in the methylase.
cross-correlation RECIPROCAL