3M0E: Transcriptional regulator

Name: PDB 3M0E: Crystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain
Published: 2010-11-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain. Determined by X-ray diffraction at 2.63 Å resolution. Released 3 Nov 2010.

Method: X-ray diffraction
Resolution: 2.63 Å
Organism: Aquifex aeolicus
Chains: 7
Atoms: 14,440
Mol. weight: 216.72 kDa
Ligands: MG, ATP
Released: 3 Nov 2010

Explore 3M0E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M0E contains 105 α-helices and 86 β-strands across 7 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-166	4	1
α-helix	173-182	10
β-strand	191-195	5	1
α-helix	201-203	3
α-helix	204-209	6
β-strand	211	1	2
β-strand	214	1	3
β-strand	218	1	3
β-strand	223	1	2
α-helix	226-229	4
β-strand	234-238	5	1
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	4
β-strand	263	1	2
β-strand	269-270	2	4
β-strand	274-279	6	1
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	1
α-helix	307-309	3
α-helix	310-312	3
α-helix	314-331	18
β-strand	338-339	2	5
α-helix	341-349	9
α-helix	355-369	15
β-strand	374-375	2	5
α-helix	377-381	5

Chains B, C, D, E, F and G: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-166	4	6
α-helix	173-182	10
β-strand	191-195	5	6
α-helix	201-203	3
α-helix	204-209	6
β-strand	211	1	7
β-strand	223	1	7
α-helix	226-229	4
β-strand	234-238	5	6
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-260	2	8
β-strand	263	1	7
β-strand	269-270	2	8
β-strand	274-279	6	6
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	6
α-helix	307-309	3
α-helix	310-312	3
α-helix	314-331	18
β-strand	338-339	2	9
α-helix	341-349	9
α-helix	355-369	15
β-strand	374-375	2	9
α-helix	377-381	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcriptional regulator (NtrC family)	A, B, C, D, E, F, G	protein	266	Aquifex aeolicus	O67198 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G), FASTA

>3M0E_1 Transcriptional regulator (NtrC family) (chains A, B, C, D, E, F, G)
RKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIH
KLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDAIG
ELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYRLG
VIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVRELKN
VIERAVLFSEGKFIDRGELSCLVNSK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	7
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	7

Primary citation

Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase for Remodeling Bacterial RNA Polymerase. Chen, B., Sysoeva, T.A., Chowdhury, S. et al. Structure (2010) 18:1420-1430. DOI 10.1016/j.str.2010.08.018 · 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…
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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