9m9d

Structural Basis of Pausing During Transcription Initiation in Mycobacterium tuberculosis

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase subunit alpha

Mycobacterium tuberculosis H37Rv

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （P9WGY9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） ECF RNA polymerase sigma factor SigE × 1 （P9WGG7） RNA polymerase-binding transcription factor CarD × 1 （P9WJG3） DNA (48-MER) × 1 DNA (48-MER) × 1 ;RNA (5'-R(CPCPCPUPCPGP*A)-3') ; × 1 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_MYCTU
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 H37Rv

UniProt P9WGY9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P9WGZ1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） ECF RNA polymerase sigma factor SigE × 1 （P9WGG7） RNA polymerase-binding transcription factor CarD × 1 （P9WJG3） DNA (48-MER) × 1 DNA (48-MER) × 1 ;RNA (5'-R(CPCPCPUPCPGP*A)-3') ; × 1 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_MYCTU
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 H37Rv

UniProt P9WGY7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P9WGZ1） DNA-directed RNA polymerase subunit beta × 1 （P9WGY9） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） ECF RNA polymerase sigma factor SigE × 1 （P9WGG7） RNA polymerase-binding transcription factor CarD × 1 （P9WJG3） DNA (48-MER) × 1 DNA (48-MER) × 1 ;RNA (5'-R(CPCPCPUPCPGP*A)-3') ; × 1 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_MYCTU
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 H37Rv

UniProt P9WGY5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P9WGZ1） DNA-directed RNA polymerase subunit beta × 1 （P9WGY9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） ECF RNA polymerase sigma factor SigE × 1 （P9WGG7） RNA polymerase-binding transcription factor CarD × 1 （P9WJG3） DNA (48-MER) × 1 DNA (48-MER) × 1 ;RNA (5'-R(CPCPCPUPCPGP*A)-3') ; × 1 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_MYCTU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–110； UniProt 1–110

ECF RNA polymerase sigma factor SigE

Mycobacterium tuberculosis H37Rv

UniProt P9WGG7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P9WGZ1） DNA-directed RNA polymerase subunit beta × 1 （P9WGY9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） RNA polymerase-binding transcription factor CarD × 1 （P9WJG3） DNA (48-MER) × 1 DNA (48-MER) × 1 ;RNA (5'-R(CPCPCPUPCPGP*A)-3') ; × 1 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	SIGE_MYCTU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–257； UniProt 1–257

RNA polymerase-binding transcription factor CarD

Mycobacterium tuberculosis H37Rv

UniProt P9WJG3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （P9WGZ1） DNA-directed RNA polymerase subunit beta × 1 （P9WGY9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） ECF RNA polymerase sigma factor SigE × 1 （P9WGG7） DNA (48-MER) × 1 DNA (48-MER) × 1 ;RNA (5'-R(CPCPCPUPCPGP*A)-3') ; × 1 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	CARD_MYCTU
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 9–169； UniProt 2–162

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	9m9d
Deposition date deposition_date	2025-03-13
Structure title title	Structural Basis of Pausing During Transcription Initiation in Mycobacterium tuberculosis
Keywords keywords	;RNA polymerase, Initiation complex, Pausing, Mycobacterium tuberculosis, Cryo-EM, TRANSCRIPTION/DNA/RNA, TRANSCRIPTION-DNA-RNA complex ;; TRANSCRIPTION/DNA/RNA
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.

9m9d__assembly_1__model_1

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

Download this curve (.dat)

9m9d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9m9d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.32 Å
Rg (electron density)	49.90 Å
Total Rg	50.07 Å
Atom count	26866
Residues	3330
Excluded volume	470370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9m9d__assembly_1__model_1`	decameric （10）	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 (11)

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	26866

MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEVAGYDVATGTWSTEGAYDEQDYAETEQL

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
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 H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	148350.4 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

MLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAYTIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYRHHHHHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
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 H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	ECF RNA polymerase sigma factor SigE
Molecular weight formula_weight	28911.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MELLGGPRVGNTESQLCVADGDDLPTYCSANSEDLNITTITTLSPTSMSHPQQVRDDQWVEPSDQLQGTAVFDATGDKATMPSWDELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQPGTFEGWLHRITTNLFLDMVRRRARIRMEALPEDYDRVPADEPNPEQIYHDARLGPDLQAALASLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRDYLAAHPEHGECAVHVNPVR

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	RNA polymerase-binding transcription factor CarD
Molecular weight formula_weight	18819.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MGHHHHHHIFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRDVVGQEGLDKVFQVLRAPHTEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQERGLSAGEKRMLAKARQILVGELALAESTDDAKAETILDEVLAAAS

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	DNA (48-MER)
Molecular weight formula_weight	14797.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CGGAACTTTTAGTGCTAATTATTGTCAAAACCATTGTCACGGATGCAG

Entity 8 Entity 8 polymer

Description description	DNA (48-MER)
Molecular weight formula_weight	14823.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

CTGCATCCGTGAGTCGAGGGTGTTCAATAATTAGCACTAAAAGTTCCG

Entity 9 Entity 9 polymer

Description description	;RNA (5'-R(CPCPCPUPCPGP*A)-3') ;
Molecular weight formula_weight	2156.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

CCCUCGA

Entity 10 Entity 10 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 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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Resolution resolution	3.29 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	75465

Structural Basis of Pausing During Transcription Initiation in Mycobacterium tuberculosis

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

ECF RNA polymerase sigma factor SigE

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-binding transcription factor CarD

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

9m9d__assembly_1__model_1

9m9d__assembly_1__model_1 | I(q)

9m9d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

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

Entity 8 Entity 8 polymer

Polymer Polymer