1NY5: Transcriptional regulator

Name: PDB 1NY5: Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
Published: 2003-11-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state. Determined by X-ray diffraction at 2.4 Å resolution. Released 11 Nov 2003.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Aquifex aeolicus
Chains: 2
Atoms: 6,545
Mol. weight: 90.05 kDa
Ligands: ADP, PO4, MG
Released: 11 Nov 2003

Explore 1NY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NY5 contains 35 α-helices and 40 β-strands across 2 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: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	10-23	14
β-strand	26-30	5	1
α-helix	33-42	10
β-strand	47-51	5	1
β-strand	53	1	2
β-strand	58	1	2
α-helix	59-69	11
β-strand	74-80	7	1
α-helix	84-91	8
β-strand	97-101	5	1
α-helix	105-133	29
α-helix	144-156	13
β-strand	163-166	4	3
α-helix	173-183	11
β-strand	191-195	5	3
α-helix	201-209	9
β-strand	211	1	4
β-strand	223	1	4
α-helix	226-229	4
β-strand	234-238	5	3
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	5
β-strand	263	1	4
β-strand	268	1	6
β-strand	269-270	2	5
β-strand	274-279	6	3
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	3
α-helix	310-312	3
α-helix	314-331	18
β-strand	338-339	2	7
α-helix	341-349	9
α-helix	355-369	15
β-strand	374-375	2	7
α-helix	377-383	7

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
α-helix	10-23	14
β-strand	26-30	5	8
α-helix	33-42	10
β-strand	43	1	6
β-strand	47-51	5	8
β-strand	53	1	9
β-strand	58	1	9
α-helix	59-69	11
β-strand	74-79	6	8
α-helix	84-92	9
β-strand	97-100	4	8
α-helix	105-134	30
α-helix	144-156	13
β-strand	163-166	4	10
α-helix	173-182	10
β-strand	191-195	5	10
α-helix	201-209	9
β-strand	211	1	11
β-strand	223	1	11
α-helix	226-229	4
β-strand	234-238	5	10
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	12
β-strand	263	1	11
β-strand	269-270	2	12
β-strand	274-279	6	10
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	10
α-helix	307-309	3
α-helix	314-331	18
β-strand	338-339	2	13
α-helix	341-349	9
α-helix	355-368	14
β-strand	374-375	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
transcriptional regulator (NtrC family)	A, B	protein	387	Aquifex aeolicus	O67198 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1NY5_1 transcriptional regulator (NtrC family) (chains A, B)
MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGL
EILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRK
LRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLI
HKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEI
GELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRL
GVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELK
NVIERAVLFSEGKFIDRGELSCLVNSK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
PO4	Phosphate ion	O4 P	4
MG	Magnesium ion	Mg	1

Water and common crystallization additives (GOL) are not listed.

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…
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…
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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