5uhe

Crystal structure of Mycobacterium tuberculosis transcription initiation complex in complex with D-AAP1

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 (strain ATCC 25618 / H37Rv)

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 （P9WGY9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） RNA polymerase sigma factor SigA × 1 （P9WGI1） ;DNA (5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTPG)-3') ; × 1 ;DNA (5'-D(CPAPTPCPCPGPTPGPAPGPTPCPCPAPGP*G)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 1 Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide × 1	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 (strain ATCC 25618 / H37Rv)

UniProt P9WGY9

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 （P9WGZ1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） RNA polymerase sigma factor SigA × 1 （P9WGI1） ;DNA (5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTPG)-3') ; × 1 ;DNA (5'-D(CPAPTPCPCPGPTPGPAPGPTPCPCPAPGP*G)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 1 Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide × 1	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 (strain ATCC 25618 / H37Rv)

UniProt P9WGY7

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 （P9WGZ1） DNA-directed RNA polymerase subunit beta × 1 （P9WGY9） DNA-directed RNA polymerase subunit omega × 1 （P9WGY5） RNA polymerase sigma factor SigA × 1 （P9WGI1） ;DNA (5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTPG)-3') ; × 1 ;DNA (5'-D(CPAPTPCPCPGPTPGPAPGPTPCPCPAPGP*G)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 1 Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide × 1	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 (strain ATCC 25618 / H37Rv)

UniProt P9WGY5

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 （P9WGZ1） DNA-directed RNA polymerase subunit beta × 1 （P9WGY9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （P9WGY7） RNA polymerase sigma factor SigA × 1 （P9WGI1） ;DNA (5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTPG)-3') ; × 1 ;DNA (5'-D(CPAPTPCPCPGPTPGPAPGPTPCPCPAPGP*G)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 1 Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide × 1	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

RNA polymerase sigma factor SigA

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt P9WGI1

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 （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） ;DNA (5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTPG)-3') ; × 1 ;DNA (5'-D(CPAPTPCPCPGPTPGPAPGPTPCPCPAPGP*G)-3') ; × 1 ZINC ION × 2 MAGNESIUM ION × 1 Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIGA_MYCTU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–528； UniProt 1–528

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	5uhe
Deposition date deposition_date	2017-01-11
Structure title title	Crystal structure of Mycobacterium tuberculosis transcription initiation complex in complex with D-AAP1
Keywords keywords	RNA polymerase complex, transcription, DNA, RNA, TRANSCRIPTION-DNA-RNA complex; TRANSCRIPTION/DNA/RNA
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.

5uhe__assembly_1__model_1

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

Download this curve (.dat)

5uhe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5uhe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.85 Å
Rg (electron density)	47.46 Å
Total Rg	47.69 Å
Atom count	25966
Residues	3278
Excluded volume	458810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5uhe__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	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	25966

MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEVAGYDVATGTWSTEGAYDEQDYAETEQL

Source Source

Source organism organism	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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 (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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 (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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 (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor SigA
Molecular weight formula_weight	57877.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MAATKASTATDEPVKRTATKSPAASASGAKTGAKRTAAKSASGSPPAKRATKPAARSVKPASAPQDTTTSTIPKRKTRAAAKSAAAKAPSARGHATKPRAPKDAQHEAATDPEDALDSVEELDAEPDLDVEPGEDLDLDAADLNLDDLEDDVAPDADDDLDSGDDEDHEDLEAEAAVAPGQTADDDEEIAEPTEKDKASGDFVWDEDESEALRQARKDAELTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD

Source Source

Source organism organism	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 6 Entity 6 polymer

Description description	;DNA (5'-D(TPAPTPAPAPTPGPGPGPAPGPCPTPGPTPCPAPCPGPGPAPTP*G)-3') ;
Molecular weight formula_weight	7160.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

TATAATGGGAGCTGTCACGGATG

Entity 7 Entity 7 polymer

Description description	;DNA (5'-D(CPAPTPCPCPGPTPGPAPGPTPCPCPAPGPG)-3') ;
Molecular weight formula_weight	4939.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CATCCGTGAGTCGAGG

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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	Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide
Molecular weight formula_weight	358.4 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	151.531 Å
Unit-cell length b length_b	162.155 Å
Unit-cell length c length_c	195.681 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	—

Resolution resolution	4.039 Å
Low-resolution limit resolution_low	49.270 Å
R factor r_factor	0.2130
R_work r_work	0.2100
R_free r_free	0.2592

Crystal structure of Mycobacterium tuberculosis transcription initiation complex in complex with D-AAP1

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 SigA

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

5uhe__assembly_1__model_1

5uhe__assembly_1__model_1 | I(q)

5uhe__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 (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 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

7. Citations (1)