Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-A non-canonical pair at position 3

Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.

RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')

DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')

DNA (5'-D(P*TP*GP*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')

MHHHHHHDYKDDDDKAPVQAADEMYDSNPHPDRRQLVSNGFEVNLPDQVEVIVRDLPDPSKVKEERTRLMGYWFVHWFDG
KLFHLRIKAGGPNVDGEHRAIRTAEHPWLLRARLDDALEEALPKYAAVKKRPFTFLAQKDELIDAAATAAGLSHRLLNSF
KVIPRFALSPKIYEPVDGTTRVGVFVTIGMRYDIEASLRDLLEAGIDLRGMYVVRRKRQPGERGLLGRVRAISDDMVQLF
EETDLASVNVNDAKLEGSKENFTRCLSALLGHNYKKLLNALDDQEAGYRTGPRFDDAVRRMGEFLAKKPIRLADNINAQV
GDRIVFSNEGQARNVRLAPKVEYVFDRTGAKSAEYAWRGLSQFGPFDRPSFANRSPRILVVYPSSTQGKVENFLSAFRDG
MGSNYSGFSKGFVDLMGLTKVEFVMCPVEVSSADRNGAHTKYNSAIEDKLAGAGEVHAGIVVLFEDHARLPDDRNPYIHT
KSLLLTLGVPTQQVRMPTVLLEPKSLQYTLQNFSIATYAKLNGTPWTVNHDKAINDELVVGMGLAELSGSRTEKRQRFVG
ITTVFAGDGSYLLGNVSKECEYEGYSDAIRESMTGILRELKKRNNWRPGDTVRVVFHAHRPLKRVDVASIVFECTREIGS
DQNIQMAFVTVSHDHPFVLIDRSERGLEAYKGSTARKGVFAPPRGAISRVGRLTRLLAVNSPQLIKRANTPLPTPLLVSL
HPDSTFKDVDYLAEQALKFTSLSWRSTLPAATPVTIFYSERIAELLGRLKSIPNWSSANLNIKLKWSRWFL

(DT)(DG)(DT)(DC)(DG)(DT)(DC)(DA)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA)(DG)(DA)(DA)(DA)
(DC)

Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)

40% MPD, 30 mM magnesium acetate, 50 mM sodium cacodylate pH 5.7

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rhodobacter sphaerodes Argounaute (RsAgo); guide RNA; target DNA; RNA-DNA heteroduplex; non-canonical base pairs and bulges, RNA BINDING PROTEIN

APVQAADEMYDSNPHPDRRQLVSNGFEVNLPDQVEVIVRDLPDPSKVKEERTRLMGYWFVHWFDGKLFHLRIKAGGPNVD
GEHRAIRTAEHPWLLRARLDDALEEALPKYAAVKKRPFTFLAQKDELIDAAATAAGLSHRLLNSFKVIPRFALSPKIYEP
VDGTTRVGVFVTIGMRYDIEASLRDLLEAGIDLRGMYVVRRKRQPGERGLLGRVRAISDDMVQLFEETDLASVNVNDAKL
EGSKENFTRCLSALLGHNYKKLLNALDDQEAGYRTGPRFDDAVRRMGEFLAKKPIRLADNINAQVGDRIVFSNEGQARNV
RLAPKVEYVFDRTGAKSAEYAWRGLSQFGPFDRPSFANRSPRILVVYPSSTQGKVENFLSAFRDGMGSNYSGFSKGFVDL
MGLTKVEFVMCPVEVSSADRNGAHTKYNSAIEDKLAGAGEVHAGIVVLFEDHARLPDDRNPYIHTKSLLLTLGVPTQQVR
MPTVLLEPKSLQYTLQNFSIATYAKLNGTPWTVNHDKAINDELVVGMGLAELSGSRTEKRQRFVGITTVFAGDGSYLLGN
VSKECEYEGYSDAIRESMTGILRELKKRNNWRPGDTVRVVFHAHRPLKRVDVASIVFECTREIGSDQNIQMAFVTVSHDH
PFVLIDRSERGLEAYKGSTARKGVFAPPRGAISRVGRLTRLLAVNSPQLIKRANTPLPTPLLVSLHPDSTFKDVDYLAEQ
ALKFTSLSWRSTLPAATPVTIFYSERIAELLGRLKSIPNWSSANLNIKLKWSRWFL