4LY6: Transcriptional regulator

Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis. Determined by X-ray diffraction at 3.6 Å resolution. Released 4 Dec 2013.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Aquifex aeolicus
Chains: 24
Atoms: 48,190
Mol. weight: 748.74 kDa
Ligands: ADP, MG, 08T
Released: 4 Dec 2013

Explore 4LY6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LY6 contains 351 α-helices and 284 β-strands across 24 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-167	5	1
α-helix	173-183	11
β-strand	191-195	5	1
α-helix	204-209	6
β-strand	211	1	2
β-strand	223	1	2
α-helix	226-229	4
β-strand	234-238	5	1
α-helix	245-249	5
α-helix	252-257	6
β-strand	259-260	2	3
β-strand	263	1	2
β-strand	269-270	2	3
β-strand	274-279	6	1
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-307	5	1
α-helix	308-309	2
α-helix	310-312	3
α-helix	317-332	16
β-strand	338-339	2	4
α-helix	341-348	8
α-helix	355-369	15
β-strand	374-375	2	4
α-helix	377-381	5

Chain B: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-166	4	5
α-helix	173-183	11
β-strand	191-194	4	5
α-helix	204-209	6
β-strand	211	1	6
β-strand	223	1	6
α-helix	226-229	4
β-strand	234-237	4	5
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	7
β-strand	263	1	6
β-strand	269-270	2	7
β-strand	274-279	6	5
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	5
α-helix	310-312	3
α-helix	317-332	16
β-strand	338-339	2	8
α-helix	341-348	8
α-helix	355-369	15
β-strand	374-375	2	8
α-helix	377-381	5

Chain C: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-166	4	9
α-helix	173-183	11
β-strand	191-195	5	9
α-helix	204-209	6
β-strand	211	1	10
β-strand	223	1	10
α-helix	226-229	4
β-strand	234-238	5	9
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	11
β-strand	263	1	10
β-strand	269-270	2	11
β-strand	274-279	6	9
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	9
α-helix	310-312	3
α-helix	317-332	16
β-strand	338-339	2	12
α-helix	341-348	8
α-helix	358-369	12
β-strand	374-375	2	12
α-helix	377-381	5

Chain D: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-166	4	13
α-helix	173-182	10
β-strand	191-195	5	13
α-helix	204-209	6
β-strand	211	1	14
β-strand	223	1	14
α-helix	226-229	4
β-strand	234-238	5	13
α-helix	240-242	3
α-helix	245-248	4
α-helix	249-251	3
α-helix	252-257	6
β-strand	259-261	3	15
β-strand	263	1	14
β-strand	268-270	3	15
β-strand	274-279	6	13
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	13
α-helix	307-309	3
α-helix	310-312	3
α-helix	317-332	16
β-strand	338-339	2	16
α-helix	341-348	8
α-helix	358-369	12
β-strand	374-375	2	16
α-helix	377-381	5

Chain E: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-167	5	17
α-helix	173-183	11
β-strand	191-195	5	17
α-helix	204-209	6
β-strand	211	1	18
β-strand	223	1	18
α-helix	226-229	4
β-strand	234-238	5	17
α-helix	240-242	3
α-helix	245-255	11
β-strand	259-261	3	19
β-strand	263	1	18
β-strand	268-270	3	19
β-strand	274-279	6	17
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-307	5	17
α-helix	308-309	2
α-helix	310-312	3
α-helix	314-316	3
α-helix	317-332	16
β-strand	338-339	2	20
α-helix	341-348	8
α-helix	358-369	12
β-strand	374-375	2	20
α-helix	377-381	5

Chain F: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-165	3	21
α-helix	173-182	10
β-strand	191-195	5	21
α-helix	201-209	9
β-strand	211	1	22
β-strand	223	1	22
α-helix	226-229	4
β-strand	234-238	5	21
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	23
β-strand	263	1	22
β-strand	269-270	2	23
β-strand	274-278	5	21
α-helix	284-288	5
α-helix	294-300	7
β-strand	303-305	3	21
α-helix	310-312	3
α-helix	314-316	3
α-helix	317-332	16
β-strand	338-339	2	24
α-helix	341-348	8
α-helix	358-369	12
β-strand	374-375	2	24
α-helix	377-381	5

Chain G: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-156	13
β-strand	163-167	5	25
α-helix	173-182	10
β-strand	191-195	5	25
α-helix	204-209	6
β-strand	211	1	26
β-strand	223	1	26
α-helix	226-229	4
β-strand	234-238	5	25
α-helix	240-242	3
α-helix	245-255	11
β-strand	259-260	2	27
β-strand	263	1	26
β-strand	269-270	2	27
β-strand	274-278	5	25
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-307	5	25
α-helix	310-312	3
α-helix	317-332	16
β-strand	338-339	2	28
α-helix	341-348	8
α-helix	358-369	12
β-strand	374-375	2	28
α-helix	377-381	5

Chain H: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-166	4	29
α-helix	173-183	11
β-strand	191-194	4	29
α-helix	204-209	6
β-strand	211	1	30
β-strand	223	1	30
α-helix	226-229	4
β-strand	234-237	4	29
α-helix	240-242	3
α-helix	245-248	4
α-helix	252-257	6
β-strand	259-260	2	31
β-strand	263	1	30
β-strand	269-270	2	31
β-strand	274-279	6	29
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	29
α-helix	307-309	3
α-helix	310-312	3
α-helix	317-332	16
β-strand	338-339	2	32
α-helix	341-348	8
α-helix	358-368	11
β-strand	374-375	2	32
α-helix	377-381	5

16 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional regulator (NtrC family)	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	protein	268	Aquifex aeolicus	O67198 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X), FASTA

>4LY6_1 Transcriptional regulator (NtrC family) (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X)
MLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARL
IHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDE
IGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYR
LGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVREL
KNVIERAVLFSEGKFIDRGELSCLVNSK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	20
08T	[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxi…	C10 H14 Be F3 N5 O10 P2	20

Primary citation

Nucleotide-induced asymmetry within ATPase activator ring drives sigma 54-RNAP interaction and ATP hydrolysis. Sysoeva, T.A., Chowdhury, S., Guo, L. et al. Genes Dev (2013) 27:2500-2511. DOI 10.1101/gad.229385.113 · PubMed

Other PDB entries of the same protein (UniProt O67198 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4L5E 1.34 Å, Crystal structure of A. aeolicus NtrC1 DNA binding domain
4L4U 2.2 Å, Crystal structure of construct containing A. aeolicus NtrC1 receiver, central and DNA…
1NY5 2.4 Å, Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
9MSF 2.6 Å, de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic…
3M0E 2.63 Å, Crystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain
9MSE 2.7 Å, de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic…
9MSG 2.7 Å, De novo SigN RNA polymerase transcription initiation intermediate with bound SigN-RII
1ZY2 3.03 Å, Crystal structure of the phosphorylated receiver domain of the transcription regulator…
1NY6 3.1 Å, Crystal structure of sigm54 activator (AAA+ ATPase) in the active state
4LZZ 3.21 Å, Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction…
4BT1 16.0 Å, MuB is an AAAplus ATPase that forms helical filaments to control target selection for…
4BT0 17.0 Å, MuB is an AAAplus ATPase that forms helical filaments to control target selection for…

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