6zca

Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer)

Method: ELECTRON MICROSCOPY

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

;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ;

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	RNA polymerase subunit omega × 1 （A0A410WI33） DNA-directed RNA polymerase subunit alpha × 2 （A0A063XB83） DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） DNA helicase × 1 （A0A164TSE8） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0D1KIU7_BACIU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–92； UniProt 1–92

RNA polymerase subunit omega

OrganismNot specified

UniProt A0A410WI33

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ; × 1 （A0A0D1KIU7） DNA-directed RNA polymerase subunit alpha × 2 （A0A063XB83） DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） DNA helicase × 1 （A0A164TSE8） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A410WI33_BACVA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–69； UniProt 1–69

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

UniProt A0A063XB83

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ; × 1 （A0A0D1KIU7） RNA polymerase subunit omega × 1 （A0A410WI33） DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） DNA helicase × 1 （A0A164TSE8） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A063XB83_BACIU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain U； PDBConstruct 1–314； UniProt 1–314 Author chain V； PDBConstruct 1–314； UniProt 1–314

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt A0A2J0WBQ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ; × 1 （A0A0D1KIU7） RNA polymerase subunit omega × 1 （A0A410WI33） DNA-directed RNA polymerase subunit alpha × 2 （A0A063XB83） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） DNA helicase × 1 （A0A164TSE8） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2J0WBQ0_BACIU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain X； PDBConstruct 1–1193； UniProt 1–1193

;DNA-directed RNA polymerase subunit beta' ;

OrganismNot specified

UniProt A0A063XB23

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ; × 1 （A0A0D1KIU7） RNA polymerase subunit omega × 1 （A0A410WI33） DNA-directed RNA polymerase subunit alpha × 2 （A0A063XB83） DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） DNA helicase × 1 （A0A164TSE8） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A063XB23_BACIU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain Y； PDBConstruct 1–1199； UniProt 1–1199

DNA helicase

OrganismNot specified

UniProt A0A164TSE8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ; × 1 （A0A0D1KIU7） RNA polymerase subunit omega × 1 （A0A410WI33） DNA-directed RNA polymerase subunit alpha × 2 （A0A063XB83） DNA-directed RNA polymerase subunit beta × 1 （A0A2J0WBQ0） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A063XB23） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A164TSE8_BACIU
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain H； PDBConstruct 1–774； UniProt 1–774

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	6zca
Deposition date deposition_date	2020-06-10
Structure title title	Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer)
Keywords keywords	TRANSCRIPTION/DNA/RNA, DNA-DEPENDENT RNA POLYMERASE, BACTERIAL, TRANSCRIPTION, Helicase; 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.

6zca__assembly_1__model_1

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

Download this curve (.dat)

6zca__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6zca__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.98 Å
Rg (electron density)	52.57 Å
Total Rg	52.72 Å
Atom count	28721
Residues	3640
Excluded volume	511210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6zca__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 (7)

Entity 1 Entity 1 polymer

Description description	;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ;
Molecular weight formula_weight	14914.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	28721

MGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 2 Entity 2 polymer

Description description	RNA polymerase subunit omega
Molecular weight formula_weight	8228.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MIYKVFYQEKADEVPVREKTDSLYIEGVSERDVRTKLKEKKLNIEFITPVNGAFLEYEQQSENFKVLEL

Entity 3 Entity 3 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	U,V

MIEIEKPKIETVEISDDAKFGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILHIKKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEILNPDLHIATLGENASFRVRLTAQRGRGYTPADANKRDDQPIGVIPIDSIYTPVSRVSYQVENTRVGQVANYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKDD

Entity 4 Entity 4 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	X

MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSIVARFRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQADGLALSGDEEPEETASADVERDVVTKE

Entity 5 Entity 5 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	Y

MLDVNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECHCGKYKRVRYKGVVCDRCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPANTPLEKKQLLSEKEYRAYLDKYGNKFQASMGAEAIHKLLQDIDLVKEVDMLKEELKTSQGQRRTRAIKRLEVLEAFRNSGNKPSWMILDVLPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPSIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMYQCGLPKEMALELFKPFVMKELVEKGLAHNIKSAKRKIERVQPEVWDVLESVIKEHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERAGAVGEGMVFKNTDEALLAYQNGYVHLHTRVAVAANSLKNVTFTEEQRSKLLITTVGKLVFNEILPESFPYMNEPTKSNIEEKTPDRFFLEKGADVKAVIAQQPINAPFKKGILGKIIAEIFKRFHITETSKMLDRMKNLGFKYSTKAGITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRGLITEEERYERVISIWSAAKDVIQGKLMKSLDELNPIYMMSDSGARGNASNFTQLAGMRGLMANPAGRIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIIRETDCGTDRGILAKPLKEGTETIERLEERLIGRFARKQVKHPETGEVLVNENELIDEDKALEIVEAGIEEVWIRSAFTCNTPHGVCKRCYGRNLATGSDVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQELFEARNPKGQATITEIDGTVVEINEVRDKQQEIVVQGAVETRSYTAPYNSRLKVAEGDKITRGQVLTEGSIDPKELLKVTDLTTVQEYLLHEVQKVYRMQGVEIGDKHVEVMVRQMLRKVRVIDAGDTDVLPGTLLDIHQFTEANKKVLLEGNRPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVIIGKLVPAGTGMMKYRKVKPVSNVQPTDDMVPVE

Entity 6 Entity 6 polymer

Description description	DNA helicase
Molecular weight formula_weight	90052.5 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MNQQDKEWKEEQSRIDEVLKELEKKERFLETSAGGLKHDIIGLRKSFWEDVKVNFDDAHEAIETMASIKQQAELLSDREHNHRRMDQQLKRIHQLKKSPYFGRIDFIENGEEQAERIYIGLASCLDEKEEHFLIYDWRAPISSLYYNYSPGKAEYEVPGETIEGEMVLKRQFMIKNGTLKAMFNTDMTIGDEMLQEVLSHHSDTQMKNIVSTIQKEQNQIIRNEKSKILIVQGAAGSGKTSAALQRVAYLLYRHRGVIDAGQIVLFSPNFLFNSYVSSVLPELGEENMEQATFQEYIEHRLGRKFKCESPFDQLEYCLTETKGGDFPTRLAGITWKAGLSFQQFINEYVTRLSSEGMIFKNIIFRGQKLITKEQIQSYFYSLDQNHSIPNRMEQTAKWLLSELNKLEKKERRKDWVVHEAELLDKEDYLDVYKKLQERKRFSESTFNDYQREQQLLAAIIVKKAFKPLKQAVRLLAFLDVTQLYLQLFSGWGGKFQHEKMDAIGELTRSAFTDNKLLYEDAAPFLYMQDLIEGRKKNTKIKHLFIDEAQDYSPFQMAYMRSIFPAASMTVLGDINQSIYAHTINGDQRMDACFEDEPAEYVRLKRTYRSTRQIVEFTKAMLQDGADIEPFNRSGEMPLVVKTEGHESLCQKLAQEIGRLKKKGHETIAVICKTAHQCIQAHAHMSEYTDVRLIHKENQPFQKGVCVIPVYLAKGIEFDAVLVYDASEEHYHTEHDRRLLYTACTRAMHMLAVFYTGEASPFVTAVPPHLYQIAE

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	1

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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	4.200 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	81279

Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer)

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

;Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta,Probable DNA-directed RNA polymerase subunit delta ;

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 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

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 helicase

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

6zca__assembly_1__model_1

6zca__assembly_1__model_1 | I(q)

6zca__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Entity 7 Entity 7 non-polymer

7. Citations (1)