9MSF: Transcriptional regulator

Name: PDB 9MSF: de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring)
Published: 2025-08-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring). Determined by electron microscopy at 2.6 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Aquifex aeolicus VF5, Escherichia coli
Chains: 16
Atoms: 44,073
Mol. weight: 743.3 kDa
Ligands: ATP, ZN, POP, ADP
Released: 13 Aug 2025

Explore 9MSF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MSF contains 274 α-helices and 300 β-strands across 12 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: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	144-156	13
β-strand	163-167	5	1
α-helix	173-182	10
β-strand	191-195	5	1
α-helix	201-203	3
α-helix	204-209	6
β-strand	210-211	2	2
β-strand	223-224	2	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	3
β-strand	269-270	2	3
β-strand	274-279	6	1
α-helix	283-289	7
α-helix	294-300	7
β-strand	304-307	4	1
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	4
α-helix	341-349	9
α-helix	355-368	14
β-strand	374-375	2	4
α-helix	377-383	7

Chain B: 15 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	191-195	5	5
α-helix	196-198	3
α-helix	201-203	3
α-helix	204-209	6
β-strand	210-211	2	6
β-strand	223-224	2	6
α-helix	226-229	4
β-strand	234-238	5	5
α-helix	240-242	3
α-helix	245-248	4
α-helix	249-251	3
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	317-331	15
β-strand	339	1	8
α-helix	341-349	9
α-helix	355-368	14
β-strand	375	1	8
α-helix	378-381	4

Chain C: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-167	5	9
α-helix	173-182	10
β-strand	191-195	5	9
α-helix	204-208	5
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	245-248	4
α-helix	249-251	3
α-helix	252-256	5
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	283-289	7
α-helix	294-300	7
β-strand	303-307	5	9
α-helix	314-316	3
α-helix	317-331	15
β-strand	338-339	2	12
α-helix	341-349	9
α-helix	355-368	14
β-strand	374-375	2	12
α-helix	377-383	7

Chain D: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-155	12
β-strand	163-166	4	13
α-helix	173-183	11
β-strand	191-195	5	13
α-helix	196-198	3
α-helix	201-203	3
α-helix	204-209	6
β-strand	210-211	2	14
β-strand	223-224	2	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	253-257	5
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	283-289	7
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	339	1	16
α-helix	341-347	7
α-helix	355-368	14
β-strand	375	1	16

Chain E: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-156	13
β-strand	163-166	4	17
α-helix	173-183	11
β-strand	191-195	5	17
α-helix	201-203	3
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	247-249	3
α-helix	252-257	6
β-strand	259-260	2	19
β-strand	263	1	18
β-strand	269-270	2	19
β-strand	274-279	6	17
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-306	4	17
α-helix	310-312	3
α-helix	318-332	15
β-strand	338-339	2	20
α-helix	341-349	9
α-helix	355-368	14
β-strand	374-375	2	20

Chain F: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	144-156	13
β-strand	163-167	5	21
α-helix	173-183	11
β-strand	191-195	5	21
α-helix	201-203	3
α-helix	204-208	5
β-strand	210-211	2	22
β-strand	223-224	2	22
α-helix	226-229	4
β-strand	234-238	5	21
α-helix	240-242	3
α-helix	245-257	13
β-strand	259-261	3	23
β-strand	263	1	22
β-strand	268-270	3	23
β-strand	274-279	6	21
α-helix	283-288	6
α-helix	294-300	7
β-strand	303-307	5	21
α-helix	310-312	3
α-helix	317-332	16
β-strand	338-339	2	24
α-helix	341-349	9
α-helix	355-369	15
β-strand	374-375	2	24
α-helix	377-383	7

Chain G: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12-18	7	25
β-strand	23-31	9	25
α-helix	35-50	16
β-strand	52-61	10	26
β-strand	74	1	27
α-helix	78-85	8
β-strand	90-92	3	28
β-strand	97-105	9	26
β-strand	108-111	4	27
α-helix	112-114	3
β-strand	115	1	26
α-helix	116-117	2
β-strand	121-123	3	28
β-strand	129-133	5	27
β-strand	139-150	12	26
β-strand	152-153	2	29
α-helix	166-167	2
β-strand	170-172	3	26
β-strand	175-176	2	29
β-strand	180-189	10	25
β-strand	199-207	9	25
α-helix	213-232	20
α-helix	251-254	4
β-strand	256	1	30
α-helix	257-259	3
α-helix	264-272	9
β-strand	277	1	30
α-helix	278-282	5
α-helix	286-291	6
α-helix	297-308	12

Chain H: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	13-20	8	31
β-strand	23-31	9	31
α-helix	35-49	15
β-strand	52-61	10	32
β-strand	74	1	33
α-helix	78-86	9
β-strand	90-92	3	34
β-strand	97-105	9	32
β-strand	108-111	4	33
α-helix	112-114	3
α-helix	116-117	2
β-strand	121-123	3	34
β-strand	129-133	5	33
β-strand	139-150	12	32
β-strand	152-153	2	35
α-helix	155-158	4
β-strand	170-172	3	32
β-strand	175-176	2	35
β-strand	180-190	11	31
β-strand	198-207	10	31
α-helix	213-226	14

4 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	protein	268	Aquifex aeolicus VF5	O67198 (AlphaFold model)
DNA-directed RNA polymerase subunit alpha	G, H	protein	329	Escherichia coli	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	I	protein	1342	Escherichia coli	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	J	protein	1415	Escherichia coli	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	K	protein	91	Escherichia coli	P0A800
RNA polymerase sigma-54 factor	M	protein	477	Escherichia coli	P24255
dhsU (-60 to +30) non-template strand	S, U	DNA	90	Aquifex aeolicus VF5
dhsU (-60 to +30) template strand	T, V	DNA	90	Aquifex aeolicus VF5

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

>9MSF_1 Transcriptional regulator (NtrC family) (chains A, B, C, D, E, F)
MLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARL
IHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDE
IGELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRNIKELVKEGKFREDLYYR
LGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSYPWYGNVREL
KNVIERAVLFSEGKFIDRGELSCLVNSK

Sequence of entity 2 (G, H), FASTA

>9MSF_2 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 3 (I), FASTA

>9MSF_3 DNA-directed RNA polymerase subunit beta (chains I)
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQ
SYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQ
EVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR
GSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME
LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRL
SALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGIL
SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS
LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTR
ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQV
VSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERG
DVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVS
RDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEK
LLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL
SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDE
LKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKIN
PIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAK
LREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK
LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG
GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMP
ESFNVLLKEIRSLGINIELEDE

Sequence of entity 4 (J), FASTA

>9MSF_4 DNA-directed RNA polymerase subunit beta' (chains J)
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELELEVLFQ

Sequence of entity 5 (K), FASTA

>9MSF_5 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 6 (M), FASTA

>9MSF_6 RNA polymerase sigma-54 factor (chains M)
MKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQIDTHEEIDTRE
TQDSETLDTADALEQKEMPEELPLDASWDTIYTAGTPSGTSGDYIDDELPVYQGETTQTL
QDYLMWQVELTPFSDTDRAIATSIVDAVDETGYLTVPLEDILESIGDEEIDIDEVEAVLK
RIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIISDHLDLLANHDFRTLMRVTR
LKEDVLKEAVNLIQSLDPRPGQSIQTGEPEYVIPDVLVRKHNGHWTVELNSDSIPRLQIN
QHYASMCNNARNDGDSQFIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEE
YMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAI
RALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV

Sequence of entity 7 (S, U), FASTA

>9MSF_7 dhsU (-60 to +30) non-template strand (chains S, U)
CGCAAGTTCCTTAGAATTTCAGTGTCCAGAAATTGGCACGAAAATTGCAATAAATACAAC
GAACAAAAATGGAGGTAAGAGTATGGGTGG

Sequence of entity 8 (T, V), FASTA

>9MSF_8 dhsU (-60 to +30) template strand (chains T, V)
CCACCCATACTCTTACCTCCATTTTTGTTCGTTGTATTTATTGCAATTTTCGTGCCAATT
TCTGGACACTGAAATTCTAAGGAACTTGCG

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	5
ZN	Zinc ion	Zn	2
POP	Pyrophosphate 2-	H2 O7 P2	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	2

Primary citation

Real-time capture of sigma N transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding. Mueller, A.U., Molina, N., Nixon, B.T. et al. Nat Commun (2025) 16:7138-7138. DOI 10.1038/s41467-025-61837-4 · 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
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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