8xa8

Cryo-EM structure of Bacillus RNAP and HelD complex

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase subunit alpha

Bacillus

UniProt P20429

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit epsilon × 1 （A0A063XGL2） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） DNA-directed RNA polymerase subunit beta × 1 （P37870） DNA-directed RNA polymerase subunit delta × 1 （P12464） 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_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' ;

Bacillus

UniProt P37871

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-directed RNA polymerase subunit alpha × 2 （P20429） DNA-directed RNA polymerase subunit epsilon × 1 （A0A063XGL2） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） DNA-directed RNA polymerase subunit beta × 1 （P37870） DNA-directed RNA polymerase subunit delta × 1 （P12464） 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_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–1199； UniProt 1–1199

DNA-directed RNA polymerase subunit epsilon

Bacillus

UniProt A0A063XGL2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） DNA-directed RNA polymerase subunit beta × 1 （P37870） DNA-directed RNA polymerase subunit delta × 1 （P12464） 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	A0A063XGL2_BACIU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–69； UniProt 1–69

DNA-directed RNA polymerase subunit omega

Bacillus

UniProt O35011

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit epsilon × 1 （A0A063XGL2） DNA helicase IV × 1 （O32215） DNA-directed RNA polymerase subunit beta × 1 （P37870） DNA-directed RNA polymerase subunit delta × 1 （P12464） 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_BACSU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–67； UniProt 1–67

DNA helicase IV

Bacillus

UniProt O32215

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit epsilon × 1 （A0A063XGL2） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA-directed RNA polymerase subunit beta × 1 （P37870） DNA-directed RNA polymerase subunit delta × 1 （P12464） 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	HELD_BACSU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain H； PDBConstruct 1–774； UniProt 1–774

DNA-directed RNA polymerase subunit beta

Bacillus

UniProt P37870

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit epsilon × 1 （A0A063XGL2） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） DNA-directed RNA polymerase subunit delta × 1 （P12464） 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_BACSU
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain C； PDBConstruct 1–1193； UniProt 1–1193

DNA-directed RNA polymerase subunit delta

Bacillus

UniProt P12464

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-directed RNA polymerase subunit alpha × 2 （P20429） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P37871） DNA-directed RNA polymerase subunit epsilon × 1 （A0A063XGL2） DNA-directed RNA polymerase subunit omega × 1 （O35011） DNA helicase IV × 1 （O32215） DNA-directed RNA polymerase subunit beta × 1 （P37870） 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	RPOE_BACSU
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain I； PDBConstruct 1–173； UniProt 1–173

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	8xa8
Deposition date deposition_date	2023-12-02
Structure title title	Cryo-EM structure of Bacillus RNAP and HelD complex
Keywords keywords	complex, 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.

8xa8__assembly_1__model_1

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

Download this curve (.dat)

8xa8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8xa8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.82 Å
Rg (electron density)	50.43 Å
Total Rg	50.59 Å
Atom count	57754
Residues	3723
Excluded volume	516700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8xa8__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-directed RNA polymerase subunit alpha
Molecular weight formula_weight	34842.4 kDa
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	57754

MIEIEKPKIETVEISDDAKFGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILHIKKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEILNPDLHIATLGENASFRVRLTAQRGRGYTPADANKRDDQPIGVIPIDSIYTPVSRVSYQVENTRVGQVANYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGLRKDD

Source Source

Source organism organism	Bacillus
NCBI taxonomy ID ncbi_taxonomy_id	1386
Host organism host_organism	Bacillus subtilis

Entity 2 Entity 2 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	134445.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLDVNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECHCGKYKRVRYKGVVCDRCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPANTPLEKKQLLSEKEYRAYLDKYGNKFQASMGAEAIHKLLQDIDLVKEVDMLKEELKTSQGQRRTRAIKRLEVLEAFRNSGNKPSWMILDVLPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPSIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMYQCGLPKEMALELFKPFVMKELVEKGLAHNIKSAKRKIERVQPEVWDVLESVIKEHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERAGAVGEGMVFKNTDEALLAYQNGYVHLHTRVAVAANSLKNVTFTEEQRSKLLITTVGKLVFNEILPESFPYMNEPTKSNIEEKTPDRFFLEKGADVKAVIAQQPINAPFKKGILGKIIAEIFKRFHITETSKMLDRMKNLGFKYSTKAGITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRGLITEEERYERVISIWSAAKDVIQGKLMKSLDELNPIYMMSDSGARGNASNFTQLAGMRGLMANPAGRIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIIRETDCGTDRGILAKPLKEGTETIERLEERLIGRFARKQVKHPETGEVLVNENELIDEDKALEIVEAGIEEVWIRSAFTCNTPHGVCKRCYGRNLATGSDVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQELFEARNPKGQATITEIDGTVVEINEVRDKQQEIVVQGAVETRSYTAPYNSRLKVAEGDKITRGQVLTEGSIDPKELLKVTDLTTVQEYLLHEVQKVYRMQGVEIGDKHVEVMVRQMLRKVRVIDAGDTDVLPGTLLDIHQFTEANKKVLLEGNRPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVIIGKLVPAGTGMMKYRKVKPVSNVQPTDDMVPVE

Source Source

Source organism organism	Bacillus
NCBI taxonomy ID ncbi_taxonomy_id	1386
Host organism host_organism	Bacillus subtilis

Entity 3 Entity 3 polymer

Description description	DNA-directed RNA polymerase subunit epsilon
Molecular weight formula_weight	8277.4 kDa
Mutation mutation	V33I
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MIYKVFYQEKADEVPVREKTDSLYIEGVSERDIRTKLKEKKFNIEFITPVDGAFLEYEQQSENFKVLEL

Source Source

Source organism organism	Bacillus
NCBI taxonomy ID ncbi_taxonomy_id	1386
Host organism host_organism	Bacillus subtilis

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	7766.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MLDPSIDSLMNKLDSKYTLVTVSARRAREMQIKKDQMIEHTISHKYVGKALEEIDAGLLSFEKEDRE

Source Source

Source organism organism	Bacillus
NCBI taxonomy ID ncbi_taxonomy_id	1386
Host organism host_organism	Bacillus subtilis

Entity 5 Entity 5 polymer

Description description	DNA helicase IV
Molecular weight formula_weight	90052.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MNQQDKEWKEEQSRIDEVLKELEKKERFLETSAGGLKHDIIGLRKSFWEDVKVNFDDAHEAIETMASIKQQAELLSDREHNHRRMDQQLKRIHQLKKSPYFGRIDFIENGEEQAERIYIGLASCLDEKEEHFLIYDWRAPISSLYYNYSPGKAEYEVPGETIEGEMVLKRQFMIKNGTLKAMFNTDMTIGDEMLQEVLSHHSDTQMKNIVSTIQKEQNQIIRNEKSKILIVQGAAGSGKTSAALQRVAYLLYRHRGVIDAGQIVLFSPNFLFNSYVSSVLPELGEENMEQATFQEYIEHRLGRKFKCESPFDQLEYCLTETKGGDFPTRLAGITWKAGLSFQQFINEYVTRLSSEGMIFKNIIFRGQKLITKEQIQSYFYSLDQNHSIPNRMEQTAKWLLSELNKLEKKERRKDWVVHEAELLDKEDYLDVYKKLQERKRFSESTFNDYQREQQLLAAIIVKKAFKPLKQAVRLLAFLDVTQLYLQLFSGWGGKFQHEKMDAIGELTRSAFTDNKLLYEDAAPFLYMQDLIEGRKKNTKIKHLFIDEAQDYSPFQMAYMRSIFPAASMTVLGDINQSIYAHTINGDQRMDACFEDEPAEYVRLKRTYRSTRQIVEFTKAMLQDGADIEPFNRSGEMPLVVKTEGHESLCQKLAQEIGRLKKKGHETIAVICKTAHQCIQAHAHMSEYTDVRLIHKENQPFQKGVCVIPVYLAKGIEFDAVLVYDASEEHYHTEHDRRLLYTACTRAMHMLAVFYTGEASPFVTAVPPHLYQIAE

Source Source

Source organism organism	Bacillus
NCBI taxonomy ID ncbi_taxonomy_id	1386
Host organism host_organism	Bacillus subtilis

Entity 6 Entity 6 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	133847.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSIVARFRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQADGLALSGDEEPEETASADVERDVVTKE

Source Source

Source organism organism	Bacillus
NCBI taxonomy ID ncbi_taxonomy_id	1386
Host organism host_organism	Bacillus subtilis

Entity 7 Entity 7 polymer

Description description	DNA-directed RNA polymerase subunit delta
Molecular weight formula_weight	20417.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK

Source Source

Source organism organism	Bacillus
NCBI taxonomy ID ncbi_taxonomy_id	1386
Host organism host_organism	Bacillus subtilis

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 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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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	3.19 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	78265

Cryo-EM structure of Bacillus RNAP and HelD 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 epsilon

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

DNA helicase IV

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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8xa8__assembly_1__model_1

8xa8__assembly_1__model_1 | I(q)

8xa8__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

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