7xl4

Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzyme complexes with transcription factor SutA (closed lobe)

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase subunit alpha

Pseudomonas aeruginosa PAO1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	DNA-directed RNA polymerase subunit beta × 1 （Q51561） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） Transcriptional factor SutA × 1 （Q9HTR9） RNA polymerase sigma factor RpoS × 1 （P45684） ZINC ION × 2 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–345； UniProt 1–333 Author chain B； PDBConstruct 13–345； UniProt 1–333

DNA-directed RNA polymerase subunit beta

Pseudomonas aeruginosa PAO1

UniProt Q51561

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	DNA-directed RNA polymerase subunit alpha × 2 （O52760） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） Transcriptional factor SutA × 1 （Q9HTR9） RNA polymerase sigma factor RpoS × 1 （P45684） ZINC ION × 2 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_PSEAE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–1359； UniProt 1–1357

;DNA-directed RNA polymerase subunit beta' ;

Pseudomonas aeruginosa PAO1

UniProt Q9HWC9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	DNA-directed RNA polymerase subunit alpha × 2 （O52760） DNA-directed RNA polymerase subunit beta × 1 （Q51561） DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） Transcriptional factor SutA × 1 （Q9HTR9） RNA polymerase sigma factor RpoS × 1 （P45684） ZINC ION × 2 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_PSEAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 3–1400； UniProt 2–1399

DNA-directed RNA polymerase subunit omega

Pseudomonas aeruginosa PAO1

UniProt Q9HTM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	DNA-directed RNA polymerase subunit alpha × 2 （O52760） DNA-directed RNA polymerase subunit beta × 1 （Q51561） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） Transcriptional factor SutA × 1 （Q9HTR9） RNA polymerase sigma factor RpoS × 1 （P45684） ZINC ION × 2 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOZ_PSEAE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–88； UniProt 1–88

Transcriptional factor SutA

Pseudomonas aeruginosa PAO1

UniProt Q9HTR9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	DNA-directed RNA polymerase subunit alpha × 2 （O52760） DNA-directed RNA polymerase subunit beta × 1 （Q51561） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） RNA polymerase sigma factor RpoS × 1 （P45684） ZINC ION × 2 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9HTR9_PSEAE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain G； PDBConstruct 5–109； UniProt 1–105

RNA polymerase sigma factor RpoS

Pseudomonas aeruginosa PAO1

UniProt P45684

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	DNA-directed RNA polymerase subunit alpha × 2 （O52760） DNA-directed RNA polymerase subunit beta × 1 （Q51561） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9HWC9） DNA-directed RNA polymerase subunit omega × 1 （Q9HTM1） Transcriptional factor SutA × 1 （Q9HTR9） ZINC ION × 2 MAGNESIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOS_PSEAE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 5–338； UniProt 1–334

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	7xl4
Deposition date deposition_date	2022-04-21
Structure title title	Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzyme complexes with transcription factor SutA (closed lobe)
Keywords keywords	transcription initiation, Pseudomonas aeruginosa, RNA polymerase, sigmaS, SutA, RNAP beta lobe, closed beta lobe, 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.

7xl4__assembly_1__model_1

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

Download this curve (.dat)

7xl4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7xl4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.58 Å
Rg (electron density)	48.82 Å
Total Rg	48.94 Å
Atom count	24560
Residues	3479
Excluded volume	433040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7xl4__assembly_1__model_1`	heptameric （7）	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 (8)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	38264.3 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	24560

MGHHHHHHHHHHMQSSVNEFLTPRHIDVQVVSQTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVVEAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQLDHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFSPVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPVVEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDKATA

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	151225.3 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGMAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKECVLRGVTFAVPLRVKVRLIIFDRESSNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKGETLNLELVPQRLRGEVASIDIKDGSGKVIVEQGRRITARHINQLEKAGVSQLEVPFDYLIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRVVVRVADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIEKMQLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEGGPALKKGTEITDDYLDGLERGQWFKLRMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQRKVAELRKFLHEIYNEIGGREENLDELGDNEILALAKNLRGGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	156038.5 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLKDLLNLLKNQGQIEEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKGQLLNDEQYFEALEEFGDDFDARMGAEAVHELLNAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVLTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEGRGMATTIKAAKKMVERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVMGLYYMTREAINAKGEGMAFADLQEVDRAYRSGQASLHARVKVRINEKIKGEDGQLTANTRIVDTTVGRALLFQVVPAGLPFDVVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTISGVSIGVNDFVIPDEKARIINAATDEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMANLSKEKVVDREGKEVDQESFNSMYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEIDCGTEHGLLMSPHIEGGDVVEPLGERVLGRVIARDVFKPGSDEVIVPAGTLIDEKWVDFLEVMSVDEVVVRSPITCETRHGICAMCYGRDLARGHRVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAADNVQVKNGGTIRLHNLKHVVRADGALVAVSRSGELAVADDFGRERERYKLPYGAVISVKEGDKVDPGAIVAKWDPHTHPIVTEVDGTVAFVGMEEGITVKRQTDELTGLTNIEVMDPKDRPAAGKDIRPAVKLIDAAGKDLLLPGTDVPAQYFLPANALVNLTDGAKVSIGDVVARIPQETSKTRDITGGLPRVADLFEARRPKEPSILAEISGTISFGKETKGKRRLVITPNDGSDPYEELIPKWRHLNVFEGEQVNRGEVISDGPSNPHDILRLLGVSSLAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSESGDSSFIKGDQVELTQVLEENEQLGTEDKFPAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSERKRQRDLGKPQRVSASEAEAALTEALNSSGNGSGSWSHPQFEK

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 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	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MARVTVEDCLDNVDNRFELVMLATKRARQLATGGKEPKVAWENDKPTVVALREIASGLVDENVVQQEDIVEDEPLFAAFDDEANTEAL

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Transcriptional factor SutA
Molecular weight formula_weight	11497.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GAMGMSEEELEQDELDGADEDDGEELAAADDGEADSGDGDEAPAPGKKAKAAVVEEELPSVEAKQKERDALAKAMEEFLSRGGKVQEIEPNVVADPPKKPDSKYGSRPI

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	RNA polymerase sigma factor RpoS
Molecular weight formula_weight	38606.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GAMGMALKKEGPEFDHDDEVLLLEPGIMLDESSADEQPSPRATPKATTSFSSKQHKHIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDALFQ

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 non-polymer

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

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

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7xl4C01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	7xl4E01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

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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	—

Resolution resolution	3.86 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	29531

Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzyme complexes with transcription factor SutA (closed lobe)

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

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

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

Transcriptional factor SutA

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 RpoS

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

7xl4__assembly_1__model_1

7xl4__assembly_1__model_1 | I(q)

7xl4__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer