9wsm

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

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit omega

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA (54-MER) × 1 DNA (50-MER) × 1 RNA polymerase sigma factor FliA × 1 （P29248） DNA-directed RNA polymerase subunit alpha × 2 （O52760） DNA-directed RNA polymerase subunit beta × 1 （Q51561） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOZ_PSEAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–88； UniProt 1–88

RNA polymerase sigma factor FliA

Pseudomonas aeruginosa

UniProt P29248

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA (54-MER) × 1 DNA (50-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） DNA-directed RNA polymerase subunit alpha × 2 （O52760） DNA-directed RNA polymerase subunit beta × 1 （Q51561） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FLIA_PSEAE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 6–252； UniProt 1–247

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

UniProt O52760

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA (54-MER) × 1 DNA (50-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） RNA polymerase sigma factor FliA × 1 （P29248） DNA-directed RNA polymerase subunit beta × 1 （Q51561） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_PSEAE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–333； UniProt 1–333 Author chain B； PDBConstruct 1–333； UniProt 1–333

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt Q51561

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA (54-MER) × 1 DNA (50-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） RNA polymerase sigma factor FliA × 1 （P29248） DNA-directed RNA polymerase subunit alpha × 2 （O52760） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_PSEAE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain C； PDBConstruct 1–1357； UniProt 1–1357

;DNA-directed RNA polymerase subunit beta' ;

OrganismNot specified

UniProt Q9HWC9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA (54-MER) × 1 DNA (50-MER) × 1 DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） RNA polymerase sigma factor FliA × 1 （P29248） DNA-directed RNA polymerase subunit alpha × 2 （O52760） DNA-directed RNA polymerase subunit beta × 1 （Q51561） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_PSEAE
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain D； PDBConstruct 1–1399； UniProt 1–1399

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

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

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9wsm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9wsm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9wsm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	49.99 Å
Rg (electron density)	49.03 Å
Total Rg	49.34 Å
Atom count	28673
Residues	3516
Excluded volume	503710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9wsm__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	DNA (54-MER)
Molecular weight formula_weight	16560.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	1
Atom count atom_count	28673

TTCTCTAAAGCTCCGCCGGGAAACGCCGATAAACACCATGAACGCGAATTCTTG

Entity 2 Entity 2 polymer

Description description	DNA (50-MER)
Molecular weight formula_weight	16622.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	2

CAAGAATTCGCGTTCAACCACATTATCGGCGTTTCCCGGCGGAGCTTTAGAGAA

Entity 3 Entity 3 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	9783.9 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MARVTVEDCLDNVDNRFELVMLATKRARQLATGGKEPKVAWENDKPTVVALREIASGLVDENVVQQEDIVEDEPLFAAFDDEANTEAL

Entity 4 Entity 4 polymer

Description description	RNA polymerase sigma factor FliA
Molecular weight formula_weight	28240.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GPLHMMTAASGVRMYSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGKGASFETYAGIRIRGAMLDEVRKGDWAPRSVHRNTRMVTDAIRAIEARTGRDAKDHEVAAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGEHGLPEDTSLSHNEPIHGLLDERFQAALADAIAKLPERERLVLALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLRARLADWRSAGS

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	36694.6 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MQSSVNEFLTPRHIDVQVVSQTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVVEAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQLDHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFSPVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPVVEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDKATA

Entity 6 Entity 6 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	151037.0 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDRESSNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKGETLNLELVPQRLRGEVASIDIKDGSGKVIVEQGRRITARHINQLEKAGVSQLEVPFDYLIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKMQLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEGGPALKKGTEITDDYLDGLERGQWFKLRMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQRKVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLRGGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE

Entity 7 Entity 7 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	154595.0 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MKDLLNLLKNQGQIEEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKGQLLNDEQYFEALEEFGDDFDARMGAEAVHELLNAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVLTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEGRGMATTIKAAKKMVERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVMGLYYMTREAINAKGEGMAFADLQEVDRAYRSGQASLHARVKVRINEKIKGEDGQLTANTRIVDTTVGRALLFQVVPAGLPFDVVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTISGVSIGVNDFVIPDEKARIINAATDEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMANLSKEKVVDREGKEVDQESFNSMYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEIDCGTEHGLLMSPHIEGGDVVEPLGERVLGRVIARDVFKPGSDEVIVPAGTLIDEKWVDFLEVMSVDEVVVRSPITCETRHGICAMCYGRDLARGHRVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAADNVQVKNGGTIRLHNLKHVVRADGALVAVSRSGELAVADDFGRERERYKLPYGAVISVKEGDKVDPGAIVAKWDPHTHPIVTEVDGTVAFVGMEEGITVKRQTDELTGLTNIEVMDPKDRPAAGKDIRPAVKLIDAAGKDLLLPGTDVPAQYFLPANALVNLTDGAKVSIGDVVARIPQETSKTRDITGGLPRVADLFEARRPKEPSILAEISGTISFGKETKGKRRLVITPNDGSDPYEELIPKWRHLNVFEGEQVNRGEVISDGPSNPHDILRLLGVSSLAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSESGDSSFIKGDQVELTQVLEENEQLGTEDKFPAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSERKRQRDLGKPQRVSASEAEAALTEALNSSGN

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	36636

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit omega

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RNA polymerase sigma factor FliA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;DNA-directed RNA polymerase subunit beta' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9wsm__assembly_1__model_1

9wsm__assembly_1__model_1 | I(q)

9wsm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

7. Citations (1)