9m7y

Cryo-EM structure of gp79-dependent RNAP promoter open complex

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase subunit beta

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	;DNA-directed RNA polymerase subunit beta' ; × 1 （C3SIA2） DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） DNA-directed RNA polymerase subunit omega × 1 （C3SM87） RNA polymerase ECF sigma factor × 1 （B0FIJ8） gp79 × 1 （B0FIP1） Non-template strand DNA × 1 Template strand DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3SIA7_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1342； UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt C3SIA2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） DNA-directed RNA polymerase subunit omega × 1 （C3SM87） RNA polymerase ECF sigma factor × 1 （B0FIJ8） gp79 × 1 （B0FIP1） Non-template strand DNA × 1 Template strand DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3SIA2_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1407； UniProt 1–1407

DNA-directed RNA polymerase subunit alpha

Escherichia coli

UniProt C3SR67

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （C3SIA2） DNA-directed RNA polymerase subunit omega × 1 （C3SM87） RNA polymerase ECF sigma factor × 1 （B0FIJ8） gp79 × 1 （B0FIP1） Non-template strand DNA × 1 Template strand DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3SR67_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–329； UniProt 1–329 Author chain D； PDBConstruct 1–329； UniProt 1–329

DNA-directed RNA polymerase subunit omega

Escherichia coli

UniProt C3SM87

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （C3SIA2） DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） RNA polymerase ECF sigma factor × 1 （B0FIJ8） gp79 × 1 （B0FIP1） Non-template strand DNA × 1 Template strand DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3SM87_ECOLX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–91； UniProt 1–91

RNA polymerase ECF sigma factor

Escherichia phage phiEco32

UniProt B0FIJ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （C3SIA2） DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） DNA-directed RNA polymerase subunit omega × 1 （C3SM87） gp79 × 1 （B0FIP1） Non-template strand DNA × 1 Template strand DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B0FIJ8_BPE32
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–214； UniProt 1–214

gp79

Escherichia phage phiEco32

UniProt B0FIP1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （C3SIA7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （C3SIA2） DNA-directed RNA polymerase subunit alpha × 2 （C3SR67） DNA-directed RNA polymerase subunit omega × 1 （C3SM87） RNA polymerase ECF sigma factor × 1 （B0FIJ8） Non-template strand DNA × 1 Template strand DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B0FIP1_BPE32
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–82； UniProt 1–82

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	9m7y
Deposition date deposition_date	2025-03-11
Last revision last_revision	2025-09-03
Structure title title	Cryo-EM structure of gp79-dependent RNAP promoter open complex
Keywords keywords	phage, transcription regulation, sigma factor, gp79, gp36, 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.

9m7y__assembly_1__model_1

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

Download this curve (.dat)

9m7y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9m7y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.43 Å
Rg (electron density)	48.41 Å
Total Rg	48.72 Å
Atom count	28130
Residues	3409
Excluded volume	494800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9m7y__assembly_1__model_1`	nonameric （9）	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 beta
Molecular weight formula_weight	150820.9 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	A
Atom count atom_count	28130

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	155366.8 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	B

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	36558.7 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	C,D

MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	10249.5 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	E

MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	RNA polymerase ECF sigma factor
Molecular weight formula_weight	25857.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MAKKTTPTRYRIHGIPIKYISNYEEFYKVNWKVVHKFFMYDIRDYHEAEDVAQEVLLNAWRFVFAKQDERVLEDEKDQEHMTYRVKNIIWSIRSNRQTVGDRRIYSIPEADMFRTPDMVDSPLEIAMDKQDSVGDPFMESRIFYFFQDLSDTMDTQKLANMFSMIFLGIPHDHIQKTIGMSHGTFYRRYAELKDLYEYVVEKHFDKEEFQGLIT

Source Source

Source organism organism	Escherichia phage phiEco32
NCBI taxonomy ID ncbi_taxonomy_id	2679905
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	gp79
Molecular weight formula_weight	9561.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MDMFSLEDLVQNGMMEQKEPLIVGSRKELRKLCEEWGITNQRMIGNQFSAIVTFLKRGDKYSMECVERIITEAQQDKGVTYL

Source Source

Source organism organism	Escherichia phage phiEco32
NCBI taxonomy ID ncbi_taxonomy_id	2679905
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Non-template strand DNA
Molecular weight formula_weight	21957.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

TTACTACTGATTGGTAGTAGATATGATAACTCTCAAATGTATATAGAGTACAATAAGAATTTGTATTTTAC

Entity 8 Entity 8 polymer

Description description	Template strand DNA
Molecular weight formula_weight	21855.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

GTAAAATACAAATTCTTATTCATGAGATTATACATTTGAGAGTTATCATATCTACTACCAATCAGTAGTAA

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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	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	230133

Cryo-EM structure of gp79-dependent RNAP promoter open complex

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

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 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 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 ECF sigma factor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

gp79

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

9m7y__assembly_1__model_1

9m7y__assembly_1__model_1 | I(q)

9m7y__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 polymer

Polymer Polymer