6xln

Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase subunit alpha

Escherichia coli O157:H7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （B7MIX3） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T8） DNA-directed RNA polymerase subunit omega × 1 （B7MFL0） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 9-nt RNA transcript × 1 CHAPSO × 2 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–329； UniProt 1–329 Author chain B； PDBConstruct 1–329； UniProt 1–329

DNA-directed RNA polymerase subunit beta

Escherichia coli O157:H7

UniProt B7MIX3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T8） DNA-directed RNA polymerase subunit omega × 1 （B7MFL0） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 9-nt RNA transcript × 1 CHAPSO × 2 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_ECO45
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1342； UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli O157:H7

UniProt P0A8T8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z6） DNA-directed RNA polymerase subunit beta × 1 （B7MIX3） DNA-directed RNA polymerase subunit omega × 1 （B7MFL0） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 9-nt RNA transcript × 1 CHAPSO × 2 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_ECO57
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1407； UniProt 1–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli O157:H7

UniProt B7MFL0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P0A7Z6） DNA-directed RNA polymerase subunit beta × 1 （B7MIX3） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A8T8） synthetic non-template strand DNA (54-MER) × 1 synthetic template strand DNA (54-MER) × 1 9-nt RNA transcript × 1 CHAPSO × 2 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOZ_ECO45
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–91； UniProt 1–91

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	6xln
Deposition date deposition_date	2020-06-28
Structure title title	Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription
Keywords keywords	Transcriptional factor, TRANSCRIPTION, TRANSFERASE-DNA complex, promoter escape, multidrug recognition; TRANSCRIPTION, TRANSFERASE/DNA
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.

6xln__assembly_1__model_1

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

Download this curve (.dat)

6xln__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6xln__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.21 Å
Rg (electron density)	47.02 Å
Total Rg	47.24 Å
Atom count	25956
Residues	3247
Excluded volume	459860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6xln__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 (10)

Entity 1 Entity 1 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	A,B
Atom count atom_count	25956

MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli O157:H7

Entity 2 Entity 2 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	C

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli O157:H7

Entity 3 Entity 3 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	D

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli O157:H7

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 O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli O157:H7

Entity 5 Entity 5 polymer

Description description	synthetic non-template strand DNA (54-MER)
Molecular weight formula_weight	16718.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

GCCTTGACCCTCCCCTAAGGGGAGGGTTTAGATTGTGTGCAGTCTGACGCGGCG

Entity 6 Entity 6 polymer

Description description	synthetic template strand DNA (54-MER)
Molecular weight formula_weight	16563.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

CGCCGCGTCAGACTGCACACAATCTAAACCCTCCCCTTAGGGGAGGGTCAAGGC

Entity 7 Entity 7 polymer

Description description	9-nt RNA transcript
Molecular weight formula_weight	2871.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

GCAGUCUGA

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli O157:H7

Entity 8 Entity 8 non-polymer

Description description	CHAPSO
Molecular weight formula_weight	631.9 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

Entity 10 Entity 10 non-polymer

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

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	6xlnA01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

Domain ID domain_id	6xlnB01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

Domain ID domain_id	6xlnC01
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	6xlnD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily	30 — RNA polymerase Rpb1 funnel domain

Domain ID domain_id	6xlnD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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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	2.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	76916

Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6xln__assembly_1__model_1

6xln__assembly_1__model_1 | I(q)

6xln__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 (10)

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

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)