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9wsm

Cryo-EM structure of Sigma28-RNAP open promoter complex from Pseudomonas aeruginosa

Method: ELECTRON MICROSCOPY D_max: 163.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wsm
deposition_date	2025-09-13
title	Cryo-EM structure of Sigma28-RNAP open promoter complex from Pseudomonas aeruginosa
keywords	P. aeruginosa, Sigma 28, RNAP, Flagella, fliC, TRANSCRIPTION; TRANSCRIPTION
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	49.99 Å
rg_electron	49.03 Å
i0	2706280000.00
molecular_weight	409960.0 kDa
excluded_volume	503710 Å³
envelope_volume	729370 Å³
shell_volume	117640 Å³
envelope_diameter	173.3 Å
shell_rg	57.17 Å
envelope_rg	48.79 Å
shape_rg	49.01 Å
total_rg	49.34 Å
total_atoms	28673
n_residues	3516
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	163.6 Å
rg_real	49.69 Å
rg_real_error	1.08 Å
i0_real	2.7060e+09
i0_real_error	5.3990e+07
rg_reciprocal	49.99 Å
i0_reciprocal	2707000000.0000
total_estimate	0.8758
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.3 Å
skewness	0.218
kurtosis	-0.346
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0001
highest_alpha	440200000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.898

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	DNA (54-MER)
formula_weight	16560.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	1
atom_count	28673

TTCTCTAAAGCTCCGCCGGGAAACGCCGATAAACACCATGAACGCGAATTCTTG

Entity 2 polymer

description	DNA (50-MER)
formula_weight	16622.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	2

CAAGAATTCGCGTTCAACCACATTATCGGCGTTTCCCGGCGGAGCTTTAGAGAA

Entity 3 polymer

description	DNA-directed RNA polymerase subunit omega
formula_weight	9783.9 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MARVTVEDCLDNVDNRFELVMLATKRARQLATGGKEPKVAWENDKPTVVALREIASGLVDENVVQQEDIVEDEPLFAAFDDEANTEAL

Entity 4 polymer

description	RNA polymerase sigma factor FliA
formula_weight	28240.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

GPLHMMTAASGVRMYSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGKGASFETYAGIRIRGAMLDEVRKGDWAPRSVHRNTRMVTDAIRAIEARTGRDAKDHEVAAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGEHGLPEDTSLSHNEPIHGLLDERFQAALADAIAKLPERERLVLALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLRARLADWRSAGS

Source

organism	Pseudomonas aeruginosa
ncbi_taxonomy_id	287
host_organism	Escherichia coli

Entity 5 polymer

description	DNA-directed RNA polymerase subunit alpha
formula_weight	36694.6 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MQSSVNEFLTPRHIDVQVVSQTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVVEAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQLDHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFSPVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPVVEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDKATA

Entity 6 polymer

description	DNA-directed RNA polymerase subunit beta
formula_weight	151037.0 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDRESSNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKGETLNLELVPQRLRGEVASIDIKDGSGKVIVEQGRRITARHINQLEKAGVSQLEVPFDYLIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKMQLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEGGPALKKGTEITDDYLDGLERGQWFKLRMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQRKVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLRGGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE

Entity 7 polymer

description	;DNA-directed RNA polymerase subunit beta' ;
formula_weight	154595.0 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MKDLLNLLKNQGQIEEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKGQLLNDEQYFEALEEFGDDFDARMGAEAVHELLNAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVLTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEGRGMATTIKAAKKMVERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVMGLYYMTREAINAKGEGMAFADLQEVDRAYRSGQASLHARVKVRINEKIKGEDGQLTANTRIVDTTVGRALLFQVVPAGLPFDVVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTISGVSIGVNDFVIPDEKARIINAATDEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMANLSKEKVVDREGKEVDQESFNSMYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEIDCGTEHGLLMSPHIEGGDVVEPLGERVLGRVIARDVFKPGSDEVIVPAGTLIDEKWVDFLEVMSVDEVVVRSPITCETRHGICAMCYGRDLARGHRVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAADNVQVKNGGTIRLHNLKHVVRADGALVAVSRSGELAVADDFGRERERYKLPYGAVISVKEGDKVDPGAIVAKWDPHTHPIVTEVDGTVAFVGMEEGITVKRQTDELTGLTNIEVMDPKDRPAAGKDIRPAVKLIDAAGKDLLLPGTDVPAQYFLPANALVNLTDGAKVSIGDVVARIPQETSKTRDITGGLPRVADLFEARRPKEPSILAEISGTISFGKETKGKRRLVITPNDGSDPYEELIPKWRHLNVFEGEQVNRGEVISDGPSNPHDILRLLGVSSLAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSESGDSSFIKGDQVELTQVLEENEQLGTEDKFPAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSERKRQRDLGKPQRVSASEAEAALTEALNSSGN

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.40 Å
resolution_method	—
num_particles	36636

fit	/app/data/saxs_computation/ws/9wsm/9wsm.fit
pddf	/app/data/pr_computation/ws/9wsm/9wsm.pr.out
profile	/app/data/saxs_computation/ws/9wsm/9wsm.dat

Cryo-EM structure of Sigma28-RNAP open promoter complex from Pseudomonas aeruginosa

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 non-polymer

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)