7rwi

Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198

Method: X-RAY DIFFRACTION

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

DNA-directed RNA polymerase subunit alpha

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （P9WGY8） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） RNA polymerase sigma factor × 1 （A0A045IR27） T DNA × 1 NT DNA × 1 ;(3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_MYCTA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–347； UniProt 1–347 Author chain B； PDBConstruct 1–347； UniProt 1–347

DNA-directed RNA polymerase subunit beta

Mycobacterium tuberculosis

UniProt P9WGY8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） RNA polymerase sigma factor × 1 （A0A045IR27） T DNA × 1 NT DNA × 1 ;(3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_MYCTO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1178； UniProt 1–1178

;DNA-directed RNA polymerase subunit beta' ;

Mycobacterium tuberculosis

UniProt A0A045J9E2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） DNA-directed RNA polymerase subunit beta × 1 （P9WGY8） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） RNA polymerase sigma factor × 1 （A0A045IR27） T DNA × 1 NT DNA × 1 ;(3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A045J9E2_MYCTX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1316； UniProt 1–1316

DNA-directed RNA polymerase subunit omega

Mycobacterium tuberculosis

UniProt A0A045H2R3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） DNA-directed RNA polymerase subunit beta × 1 （P9WGY8） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） RNA polymerase sigma factor × 1 （A0A045IR27） T DNA × 1 NT DNA × 1 ;(3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A045H2R3_MYCTX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–110； UniProt 1–110

RNA polymerase sigma factor

Mycobacterium tuberculosis

UniProt A0A045IR27

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） DNA-directed RNA polymerase subunit beta × 1 （P9WGY8） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A0A045J9E2） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） T DNA × 1 NT DNA × 1 ;(3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A045IR27_MYCTX
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–177； UniProt 1–177

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	7rwi
Deposition date deposition_date	2021-08-19
Structure title title	Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198
Keywords keywords	;Mycobacterium tuberculosis, RNA polymerase, transcription inhibitor, TNP-2198, open promoter complex, TRANSCRIPTION-INHIBITOR complex ;; TRANSCRIPTION/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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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.

7rwi__assembly_1__model_1

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

Download this curve (.dat)

7rwi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7rwi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.97 Å
Rg (electron density)	46.54 Å
Total Rg	46.76 Å
Atom count	24903
Residues	3141
Excluded volume	439580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7rwi__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 (8)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	37745.3 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	24903

MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEVAGYDVATGTWSTEGAYDEQDYAETEQL

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	130018.8 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	C

MLEGCILADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	146969.0 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

MLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAYTIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYR

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	11851.1 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

MSISQSDASLAAVPAVDQFDPSSGASGGYDTPLGITNPPIDELLDRVSSKYALVIYAAKRARQINDYYNQLGEGILEYVGPLVEPGLQEKPLSIALREIHADLLEHTEGE

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor
Molecular weight formula_weight	19563.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MARVSGAAAAEAALMRALYDEHAAVLWRYALRLTGDAAQAEDVVQETLLRAWQHPEVIGDTARPARAWLFTVARNMIIDERRSARFRNVVGSTDQSGTPEQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVTR

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	T DNA
Molecular weight formula_weight	7113.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CCTGCATCCGTGAGTCGAGGGTG

Entity 7 Entity 7 polymer

Description description	NT DNA
Molecular weight formula_weight	8373.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

CGTGTCAGTAGCTGTCACGGATGCAGG

Entity 8 Entity 8 non-polymer

Description description	;(3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate ;
Molecular weight formula_weight	950.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7rwiB01
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	7rwiD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

Domain ID domain_id	7rwiD02
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

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Unit-cell length a length_a	142.773 Å
Unit-cell length b length_b	160.613 Å
Unit-cell length c length_c	238.646 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	3.700 Å
Low-resolution limit resolution_low	48.710 Å
R factor r_factor	0.2093
R_work r_work	0.2080
R_free r_free	0.2451

Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198

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

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

7rwi__assembly_1__model_1

7rwi__assembly_1__model_1 | I(q)

7rwi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)