9e88

De novo backtracked transcription elongation complex of Mycobacterium tuberculosis RNA polymerase on a linear DNA fragment (TEC-Backtracked)

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

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （A5U052） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A675） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD × 1 （P9WJG2,Q12306） DNA (27-MER) × 1 ;RNA (5'-R(PGPCPGPAPGPAPGPGPGPAPCPAPCPG)-3') ; × 1 DNA (33-MER) × 1 ZINC ION × 2 MAGNESIUM ION × 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 A5U052

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A675） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD × 1 （P9WJG2,Q12306） DNA (27-MER) × 1 ;RNA (5'-R(PGPCPGPAPGPAPGPGPGPAPCPAPCPG)-3') ; × 1 DNA (33-MER) × 1 ZINC ION × 2 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_MYCTA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1177； UniProt 1–1177

;DNA-directed RNA polymerase subunit beta' ;

Mycobacterium tuberculosis

UniProt P0A675

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） DNA-directed RNA polymerase subunit beta × 1 （A5U052） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD × 1 （P9WJG2,Q12306） DNA (27-MER) × 1 ;RNA (5'-R(PGPCPGPAPGPAPGPGPGPAPCPAPCPG)-3') ; × 1 DNA (33-MER) × 1 ZINC ION × 2 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_MYCBO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 10–1325； 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	Insufficient information	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） DNA-directed RNA polymerase subunit beta × 1 （A5U052） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A675） Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD × 1 （P9WJG2,Q12306） DNA (27-MER) × 1 ;RNA (5'-R(PGPCPGPAPGPAPGPGPGPAPCPAPCPG)-3') ; × 1 DNA (33-MER) × 1 ZINC ION × 2 MAGNESIUM ION × 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

Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD

Mycobacterium tuberculosis

UniProt P9WJG2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） DNA-directed RNA polymerase subunit beta × 1 （A5U052） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A675） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） DNA (27-MER) × 1 ;RNA (5'-R(PGPCPGPAPGPAPGPGPGPAPCPAPCPG)-3') ; × 1 DNA (33-MER) × 1 ZINC ION × 2 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CARD_MYCTO
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 124–285； UniProt 1–162

Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD

Mycobacterium tuberculosis

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A5U8D3） DNA-directed RNA polymerase subunit beta × 1 （A5U052） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P0A675） DNA-directed RNA polymerase subunit omega × 1 （A0A045H2R3） DNA (27-MER) × 1 ;RNA (5'-R(PGPCPGPAPGPAPGPGPGPAPCPAPCPG)-3') ; × 1 DNA (33-MER) × 1 ZINC ION × 2 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 25–122； UniProt 1–98

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	9e88
Deposition date deposition_date	2024-11-05
Structure title title	De novo backtracked transcription elongation complex of Mycobacterium tuberculosis RNA polymerase on a linear DNA fragment (TEC-Backtracked)
Keywords keywords	RNA polymerase, transcription, promoter escape, De novo, 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.

9e88__assembly_1__model_1

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

Download this curve (.dat)

9e88__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9e88__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.82 Å
Rg (electron density)	46.66 Å
Total Rg	46.82 Å
Atom count	48635
Residues	3059
Excluded volume	432750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9e88__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 (10)

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	48635

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	129905.7 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

MEGCILADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA

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	148883.0 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

LARHGGSGAMLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAYTIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYRHHHHHHHH

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	Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD
Molecular weight formula_weight	32104.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MGHHHHHHHHHHSSGHIEGRHMASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSMIFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRDVVGQEGLDKVFQVLRAPHTEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQERGLSAGEKRMLAKARQILVGELALAESTDDAKAETILDEVLAAAS

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	DNA (27-MER)
Molecular weight formula_weight	39318.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

CTTAAAAGATTAATTTAAAATTTATCAAAAAGAGTATTGACTTAAAGTCTAACCTATAGGATACTTACAGCCAGCGAGAGGGACACGGCGAATAGCCATCCCAATCGACACCGGGGTCGGGATCTGG

Entity 7 Entity 7 polymer

Description description	;RNA (5'-R(PGPCPGPAPGPAPGPGPGPAPCPAPCPG)-3') ;
Molecular weight formula_weight	6893.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

AGCGAGAGGGACACGGCGAAU

Entity 8 Entity 8 polymer

Description description	DNA (33-MER)
Molecular weight formula_weight	39053.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

CCAGATCCCGACCCCGGTGTCGATTGGGATGGCTATTCGCCGTGTCCCTCTCGCTGGCTGTAAGTATCCTATAGGTTAGACTTTAAGTCAATACTCTTTTTGATAAATTTTAAATTAATCTTTTAAG

Entity 9 Entity 9 non-polymer

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

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

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Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	40816

De novo backtracked transcription elongation complex of Mycobacterium tuberculosis RNA polymerase on a linear DNA fragment (TEC-Backtracked)

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

Ubiquitin-like protein SMT3,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

Ubiquitin-like protein SMT3,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

9e88__assembly_1__model_1

9e88__assembly_1__model_1 | I(q)

9e88__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 (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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 non-polymer