7ckq

The cryo-EM structure of B. subtilis BmrR transcription activation complex

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

UniProt P20429

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） DNA (50-MER) × 1 DNA (50-MER) × 1 Multidrug-efflux transporter 1 regulator × 2 （P39075） UPF0356 protein YkzG × 1 （O31718） MAGNESIUM ION × 1 ZINC ION × 2 TETRAPHENYLPHOSPHONIUM × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–314； UniProt 1–314 Author chain B； PDBConstruct 1–314； UniProt 1–314

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt P37870

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） DNA (50-MER) × 1 DNA (50-MER) × 1 Multidrug-efflux transporter 1 regulator × 2 （P39075） UPF0356 protein YkzG × 1 （O31718） MAGNESIUM ION × 1 ZINC ION × 2 TETRAPHENYLPHOSPHONIUM × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1193； UniProt 1–1193

;DNA-directed RNA polymerase subunit beta' ;

OrganismNot specified

UniProt P37871

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） DNA (50-MER) × 1 DNA (50-MER) × 1 Multidrug-efflux transporter 1 regulator × 2 （P39075） UPF0356 protein YkzG × 1 （O31718） MAGNESIUM ION × 1 ZINC ION × 2 TETRAPHENYLPHOSPHONIUM × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_BACSU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1199； UniProt 1–1199

DNA-directed RNA polymerase subunit omega

OrganismNot specified

UniProt O35011

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） RNA polymerase sigma factor SigA × 1 （P06224） DNA (50-MER) × 1 DNA (50-MER) × 1 Multidrug-efflux transporter 1 regulator × 2 （P39075） UPF0356 protein YkzG × 1 （O31718） MAGNESIUM ION × 1 ZINC ION × 2 TETRAPHENYLPHOSPHONIUM × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOZ_BACSU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–67； UniProt 1–67

RNA polymerase sigma factor SigA

OrganismNot specified

UniProt P06224

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA (50-MER) × 1 DNA (50-MER) × 1 Multidrug-efflux transporter 1 regulator × 2 （P39075） UPF0356 protein YkzG × 1 （O31718） MAGNESIUM ION × 1 ZINC ION × 2 TETRAPHENYLPHOSPHONIUM × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIGA_BACSU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–371； UniProt 1–371

Multidrug-efflux transporter 1 regulator

Bacillus subtilis (strain 168)

UniProt P39075

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） DNA (50-MER) × 1 DNA (50-MER) × 1 UPF0356 protein YkzG × 1 （O31718） MAGNESIUM ION × 1 ZINC ION × 2 TETRAPHENYLPHOSPHONIUM × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BMRR_BACSU
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain G； PDBConstruct 5–282； UniProt 1–278 Author chain I； PDBConstruct 5–282； UniProt 1–278

UPF0356 protein YkzG

OrganismNot specified

UniProt O31718

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit beta × 1 （P37870） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） RNA polymerase sigma factor SigA × 1 （P06224） DNA (50-MER) × 1 DNA (50-MER) × 1 Multidrug-efflux transporter 1 regulator × 2 （P39075） MAGNESIUM ION × 1 ZINC ION × 2 TETRAPHENYLPHOSPHONIUM × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YKZG_BACSU
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain H； PDBConstruct 1–69； UniProt 1–69

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	7ckq
Deposition date deposition_date	2020-07-18
Structure title title	The cryo-EM structure of B. subtilis BmrR transcription activation complex
Keywords keywords	RNA polymerase, Transcription activation, 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.

7ckq__assembly_1__model_1

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

Download this curve (.dat)

7ckq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ckq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.29 Å
Rg (electron density)	52.50 Å
Total Rg	52.57 Å
Atom count	27484
Residues	3675
Excluded volume	479420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ckq__assembly_1__model_1`	undecameric （11）	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 (12)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	34842.4 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
Atom count atom_count	27484

MIEIEKPKIETVEISDDAKFGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILHIKKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEILNPDLHIATLGENASFRVRLTAQRGRGYTPADANKRDDQPIGVIPIDSIYTPVSRVSYQVENTRVGQVANYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKDD

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	133847.9 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	C

MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSIVARFRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQADGLALSGDEEPEETASADVERDVVTKE

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	134445.0 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

MLDVNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECHCGKYKRVRYKGVVCDRCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPANTPLEKKQLLSEKEYRAYLDKYGNKFQASMGAEAIHKLLQDIDLVKEVDMLKEELKTSQGQRRTRAIKRLEVLEAFRNSGNKPSWMILDVLPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPSIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMYQCGLPKEMALELFKPFVMKELVEKGLAHNIKSAKRKIERVQPEVWDVLESVIKEHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERAGAVGEGMVFKNTDEALLAYQNGYVHLHTRVAVAANSLKNVTFTEEQRSKLLITTVGKLVFNEILPESFPYMNEPTKSNIEEKTPDRFFLEKGADVKAVIAQQPINAPFKKGILGKIIAEIFKRFHITETSKMLDRMKNLGFKYSTKAGITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRGLITEEERYERVISIWSAAKDVIQGKLMKSLDELNPIYMMSDSGARGNASNFTQLAGMRGLMANPAGRIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIIRETDCGTDRGILAKPLKEGTETIERLEERLIGRFARKQVKHPETGEVLVNENELIDEDKALEIVEAGIEEVWIRSAFTCNTPHGVCKRCYGRNLATGSDVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQELFEARNPKGQATITEIDGTVVEINEVRDKQQEIVVQGAVETRSYTAPYNSRLKVAEGDKITRGQVLTEGSIDPKELLKVTDLTTVQEYLLHEVQKVYRMQGVEIGDKHVEVMVRQMLRKVRVIDAGDTDVLPGTLLDIHQFTEANKKVLLEGNRPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVIIGKLVPAGTGMMKYRKVKPVSNVQPTDDMVPVE

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	7766.9 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

MLDPSIDSLMNKLDSKYTLVTVSARRAREMQIKKDQMIEHTISHKYVGKALEEIDAGLLSFEKEDRE

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor SigA
Molecular weight formula_weight	43007.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MADKQTHETELTFDQVKEQLTESGKKRGVLTYEEIAERMSSFEIESDQMDEYYEFLGEQGVELISENEETEDPNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAQKIEEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE

Entity 6 Entity 6 polymer

Description description	DNA (50-MER)
Molecular weight formula_weight	15489.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	1

GTTGACTCTCCCCTAGGAGGAGGTCTTATAATGGGAGCTGTCACGGATGC

Entity 7 Entity 7 polymer

Description description	DNA (50-MER)
Molecular weight formula_weight	15485.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	2

GCATCCGTGAGTCGAGGGTAATAAAGACCTCCTCCTAGGGGAGAGTCAAC

Entity 8 Entity 8 polymer

Description description	Multidrug-efflux transporter 1 regulator
Molecular weight formula_weight	32951.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,I

GAMAMKESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIRIAE

Source Source

Source organism organism	Bacillus subtilis (strain 168)
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 9 Entity 9 polymer

Description description	UPF0356 protein YkzG
Molecular weight formula_weight	8263.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MIYKVFYQEKADEVPVREKTDSLYIEGVSERDVRTKLKEKKFNIEFITPVDGAFLEYEQQSENFKVLEL

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

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

Entity 12 Entity 12 non-polymer

Description description	TETRAPHENYLPHOSPHONIUM
Molecular weight formula_weight	339.4 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	—

Resolution resolution	4.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	103226

The cryo-EM structure of B. subtilis BmrR transcription activation complex

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

RNA polymerase sigma factor SigA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Multidrug-efflux transporter 1 regulator

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

UPF0356 protein YkzG

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

7ckq__assembly_1__model_1

7ckq__assembly_1__model_1 | I(q)

7ckq__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 (12)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer