1NY6: Transcriptional regulator

Name: PDB 1NY6: Crystal structure of sigm54 activator (AAA+ ATPase) in the active state
Published: 2003-11-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of sigm54 activator (AAA+ ATPase) in the active state. Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Nov 2003.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Aquifex aeolicus
Chains: 14
Atoms: 28,041
Mol. weight: 434.64 kDa
Ligands: ADP
Released: 11 Nov 2003

Explore 1NY6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NY6 contains 197 α-helices and 166 β-strands across 14 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, 11 β-strands

Element	Residues	Length	Sheet
α-helix	144-157	14
β-strand	163-167	5	1
α-helix	173-182	10
β-strand	191-194	4	1
α-helix	201-209	9
β-strand	210	1	2
β-strand	224	1	2
α-helix	226-229	4
β-strand	234-237	4	1
α-helix	240-242	3
α-helix	245-256	12
β-strand	259-261	3	3
β-strand	268-270	3	3
β-strand	274-279	6	1
α-helix	283-289	7
α-helix	294-300	7
β-strand	303-307	5	1
α-helix	308-309	2
α-helix	310-312	3
α-helix	314-331	18
β-strand	338-339	2	4
α-helix	341-349	9
α-helix	356-369	14
β-strand	374-375	2	4
α-helix	377-381	5

Chain B: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	146-156	11
α-helix	173-183	11
β-strand	191-195	5	5
α-helix	196-198	3
α-helix	203-209	7
β-strand	211	1	6
α-helix	226-229	4
β-strand	234-238	5	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	274-275	2	5
β-strand	278	1	5
α-helix	283-288	6
α-helix	294-300	7
α-helix	301-303	3
α-helix	314-331	18
β-strand	338-339	2	8
α-helix	341-349	9
α-helix	355-368	14
β-strand	374-375	2	8
α-helix	377-380	4

Chain C: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
α-helix	156-158	3
β-strand	163-166	4	9
α-helix	173-182	10
β-strand	192-194	3	9
α-helix	196-198	3
α-helix	204-209	6
β-strand	211	1	10
α-helix	226-229	4
β-strand	234-238	5	9
α-helix	240-242	3
α-helix	245-256	12
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	284-288	5
α-helix	294-300	7
β-strand	303-306	4	9
α-helix	310-312	3
α-helix	314-331	18
β-strand	338-339	2	12
α-helix	341-349	9
α-helix	355-368	14
β-strand	374-375	2	12
α-helix	377-381	5

Chain D: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	144-157	14
β-strand	163-166	4	13
α-helix	173-183	11
β-strand	193-194	2	14
α-helix	201-209	9
β-strand	211	1	15
α-helix	226-230	5
β-strand	236-237	2	14
α-helix	240-242	3
α-helix	245-256	12
β-strand	259-260	2	16
β-strand	263	1	15
β-strand	269-270	2	16
β-strand	279	1	13
α-helix	283-289	7
α-helix	294-301	8
β-strand	303-306	4	13
α-helix	307-309	3
α-helix	310-312	3
α-helix	314-331	18
α-helix	341-347	7
α-helix	356-359	4
α-helix	361-368	8
α-helix	377-381	5

Chain E: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	144-156	13
β-strand	165	1	17
α-helix	173-182	10
β-strand	191-192	2	18
β-strand	195	1	19
α-helix	201-209	9
β-strand	210	1	20
β-strand	211	1	21
α-helix	223	1
β-strand	224	1	20
α-helix	225	1
α-helix	226-229	4
β-strand	234-235	2	18
β-strand	238	1	19
α-helix	245-257	13
β-strand	259-261	3	22
β-strand	263	1	21
β-strand	268-270	3	22
β-strand	274-275	2	18
β-strand	278	1	19
α-helix	283-289	7
α-helix	294-300	7
α-helix	301-303	3
β-strand	305	1	17
α-helix	314-331	18
β-strand	338-339	2	23
α-helix	341-349	9
α-helix	355-369	15
β-strand	374-375	2	23

Chain F: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	144-157	14
β-strand	163-166	4	24
α-helix	173-181	9
β-strand	191-195	5	24
α-helix	201-209	9
β-strand	211	1	25
β-strand	213	1	26
β-strand	220	1	26
α-helix	225-229	5
β-strand	234-238	5	24
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-261	3	27
β-strand	263	1	25
β-strand	268-270	3	27
β-strand	274-279	6	24
α-helix	283-289	7
α-helix	294-300	7
β-strand	303-306	4	24
α-helix	310-312	3
α-helix	314-316	3
α-helix	317-332	16
β-strand	338-339	2	28
α-helix	341-346	6
α-helix	357-369	13
β-strand	374-375	2	28
α-helix	377-380	4

Chain G: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	144-156	13
β-strand	163-166	4	29
α-helix	173-183	11
β-strand	191-195	5	29
α-helix	204-207	4
β-strand	211	1	30
β-strand	223	1	30
α-helix	226-229	4
β-strand	234-238	5	29
α-helix	240-242	3
α-helix	245-256	12
β-strand	259-260	2	31
β-strand	269-270	2	31
β-strand	274-279	6	29
α-helix	283-289	7
α-helix	294-300	7
β-strand	303-306	4	29
α-helix	307-309	3
α-helix	310-312	3
α-helix	314-331	18
β-strand	338-339	2	32
α-helix	341-347	7
α-helix	357-368	12
β-strand	374-375	2	32
α-helix	377-381	5

Chain H: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	145-157	13
β-strand	165-167	3	33
α-helix	173-183	11
β-strand	191-195	5	34
α-helix	201-207	7
β-strand	211	1	35
β-strand	223	1	35
α-helix	224-225	2
α-helix	226-229	4
β-strand	234-238	5	34
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	36
β-strand	263	1	35
β-strand	269-270	2	36
β-strand	274-275	2	34
β-strand	278	1	34
α-helix	283-288	6
α-helix	294-299	6
β-strand	305-307	3	33
α-helix	310-312	3
α-helix	314-330	17
β-strand	339	1	37
α-helix	341-349	9
α-helix	357-366	10
β-strand	375	1	37
α-helix	377-380	4

6 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	protein	267	Aquifex aeolicus	O67198 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N), FASTA

>1NY6_1 transcriptional regulator (NtrC family) (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N)
MRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLI
HKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEI
GELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRL
GVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELK
NVIERAVLFSEGKFIDRGELSCLVNSK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	14

Primary citation

Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Lee, S.Y., de la Torre, A., Yan, D. et al. Genes Dev (2003) 17:2552-2563. DOI 10.1101/gad.1125603 · 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…
4LZZ 3.21 Å, Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction…
4LY6 3.6 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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