DynDom - Protein Domain Motions

RNA Polymerase Beta Subunit

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

Property	Value
Name	RNA Polymerase Beta Subunit
Conformer 1 (PDB)	1iw7 (C)
Conformer 2 (PDB)	1l9z (C)
Window Length	15
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	1046	3.35	9 - 473 476 - 491 509 - 510 516 - 1109
2	24	9.42	474 - 475 492 - 508 511 - 515

Sequence

`________________________________________________________________________________________________________________________` `1iw7(C) : MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPL` `:` `1l9z(C) : EIKRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKRENVGIQAAFKETFPIEE------gLVLDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(C) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT` `:` `1l9z(C) : MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETLVRELS-------gLLDEAVLAMRPEEAMVRLFT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(C) : LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERML` `:` `1l9z(C) : LLRPG--------lAYLFGLLADPKRYDLGEAGRYKAEEKLGVGLSGRTLV------fKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMV` `________________________________________________________________________________________________________________________` `______________________________________________________________________________________________________________473_______` `1iw7(C) : MGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT` `:` `1l9z(C) : MGSPDTLTPAKLVNSRPLEAALREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIRTPYRRVKNGVVT` `______________________________________________________________________________________________________________473_______` `_________________________508____515_____________________________________________________________________________________` `1iw7(C) : DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED` `:` `1l9z(C) : EEVVYMTASEEDRYTIAQANTPLEGDRIATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED` `_________________________508____515_____________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(C) : GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE` `:` `1l9z(C) : GEVVKVDGTRIAVRYEDGRLV-HPLRRYARSNQGTAFDQRPRVRVGQRV---dLLADGPASEEGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(C) : RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA` `:` `1l9z(C) : RITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(C) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE` `:` `1l9z(C) : NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSPE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1iw7(C) : EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPS` `:` `1l9z(C) : EQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIKGEDVPEPS` `________________________________________________________________________________________________________________________` `_______________________________________` `1iw7(C) : VPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR` `:` `1l9z(C) : VPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLA**` `_______________________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	75.1
Translation (A)	-1.6
Closure (%)	92.2
Bending Residues ( green )	473 - 492 508 - 511 515 - 532
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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