2a6h

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin

Method: X-RAY DIFFRACTION

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

DNA-directed RNA polymerase alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase omega chain × 1 （Q8RQE7） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase omega chain × 1 （Q8RQE7） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–315； UniProt 1–315 Author chain B； PDBConstruct 1–315； UniProt 1–315 Author chain K； PDBConstruct 1–315； UniProt 1–315 Author chain L； PDBConstruct 1–315； UniProt 1–315

DNA-directed RNA polymerase beta chain

OrganismNot specified

UniProt Q8RQE9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase omega chain × 1 （Q8RQE7） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase omega chain × 1 （Q8RQE7） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1119； UniProt 1–1119 Author chain M； PDBConstruct 1–1119； UniProt 1–1119

;DNA-directed RNA polymerase beta' chain ;

OrganismNot specified

UniProt Q8RQE8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） RNA polymerase omega chain × 1 （Q8RQE7） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） RNA polymerase omega chain × 1 （Q8RQE7） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_THET8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1524； UniProt 1–1524 Author chain N； PDBConstruct 1–1524； UniProt 1–1524

RNA polymerase omega chain

OrganismNot specified

UniProt Q8RQE7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase sigma factor rpoD × 1 （Q5SKW1） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOZ_THET8
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–99； UniProt 1–99 Author chain O； PDBConstruct 1–99； UniProt 1–99

RNA polymerase sigma factor rpoD

OrganismNot specified

UniProt Q5SKW1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase omega chain × 1 （Q8RQE7） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	DNA-directed RNA polymerase alpha chain × 2 （Q5SHR6） DNA-directed RNA polymerase beta chain × 1 （Q8RQE9） ;DNA-directed RNA polymerase beta' chain ; × 1 （Q8RQE8） RNA polymerase omega chain × 1 （Q8RQE7） STREPTOLYDIGIN × 1 ZINC ION × 2 MAGNESIUM ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SKW1_THET8
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–423； UniProt 1–423 Author chain P； PDBConstruct 1–423； UniProt 1–423

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	2a6h
Deposition date deposition_date	2005-07-02
Structure title title	Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin
Keywords keywords	;RNA POLYMERASE HOLOENZYME, STREPTOLYDIGIN, ANTIBIOTIC, TRANSCRIPTION REGULATION, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSFERASE ;; TRANSFERASE
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.

2a6h__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2a6h__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2a6h__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	50.42 Å
Rg (electron density)	50.13 Å
Total Rg	50.26 Å
Atom count	26755
Residues	3398
Excluded volume	477820 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2a6h__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2a6h__assembly_2__model_1`	hexameric （6）	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 (9)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase alpha chain
Molecular weight formula_weight	35056.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,K,L
Atom count atom_count	60908

MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLKE

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase beta chain
Molecular weight formula_weight	125436.5 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,M

MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase beta' chain ;
Molecular weight formula_weight	170997.4 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,N

MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEAKERPAARRGVKREQPGKQA

Entity 4 Entity 4 polymer

Description description	RNA polymerase omega chain
Molecular weight formula_weight	11521.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,O

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFGENLVPEDRLQKEMERIYPGEREE

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor rpoD
Molecular weight formula_weight	48568.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,P

MKKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

Entity 6 Entity 6 non-polymer

Description description	STREPTOLYDIGIN
Molecular weight formula_weight	600.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7398

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6. Fold Classification (SCOP + CATH) 60 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d2a6ha1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	d2a6ha2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

Domain ID domain_id	d2a6hb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	d2a6hb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

Domain ID domain_id	d2a6hc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.1 — RNA-polymerase beta

Domain ID domain_id	d2a6hd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.2 — RNA-polymerase beta-prime

Domain ID domain_id	d2a6he_
Class class	a — All alpha proteins
Fold Fold fold	a.143 — RPB6/omega subunit-like
Superfamily Superfamily superfamily	a.143.1 — RPB6/omega subunit-like
Family Family family	a.143.1.1 — RNA polymerase omega subunit

Domain ID domain_id	d2a6hf1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family family	a.4.13.1 — Sigma3 domain

Domain ID domain_id	d2a6hf2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family family	a.4.13.2 — Sigma4 domain

Domain ID domain_id	d2a6hf3
Class class	a — All alpha proteins
Fold Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

Domain ID domain_id	d2a6hk1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	d2a6hk2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

Domain ID domain_id	d2a6hl1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	d2a6hl2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

Domain ID domain_id	d2a6hm_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.1 — RNA-polymerase beta

Domain ID domain_id	d2a6hn_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.2 — RNA-polymerase beta-prime

Domain ID domain_id	d2a6ho_
Class class	a — All alpha proteins
Fold Fold fold	a.143 — RPB6/omega subunit-like
Superfamily Superfamily superfamily	a.143.1 — RPB6/omega subunit-like
Family Family family	a.143.1.1 — RNA polymerase omega subunit

Domain ID domain_id	d2a6hp1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family family	a.4.13.1 — Sigma3 domain

Domain ID domain_id	d2a6hp2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family family	a.4.13.2 — Sigma4 domain

Domain ID domain_id	d2a6hp3
Class class	a — All alpha proteins
Fold Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

CATH v4.4 (40 domains)

Domain ID domain_id	2a6hA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	2a6hA02
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	2a6hB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	2a6hB02
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	2a6hC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, subunit 2, domain 6

Domain ID domain_id	2a6hC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1100 — Rna Polymerase Beta Subunit; Chain: C,domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2a6hC03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

Domain ID domain_id	2a6hC04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	150 — Rna Polymerase Beta Subunit; Chain: C, domain 4
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, beta subunit, external 1 domain

Domain ID domain_id	2a6hC05
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

Domain ID domain_id	2a6hC06
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	2a6hD03
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

Domain ID domain_id	2a6hD04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2a6hD05
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	2a6hD06
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	2a6hD08
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

Domain ID domain_id	2a6hD09
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	280 —

Domain ID domain_id	2a6hE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

Domain ID domain_id	2a6hF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1810 —

Domain ID domain_id	2a6hF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2a6hF03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2a6hK01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	2a6hK02
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	2a6hL01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	2a6hL02
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	2a6hM01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, subunit 2, domain 6

Domain ID domain_id	2a6hM02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1100 — Rna Polymerase Beta Subunit; Chain: C,domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2a6hM03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

Domain ID domain_id	2a6hM04
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	150 — Rna Polymerase Beta Subunit; Chain: C, domain 4
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, beta subunit, external 1 domain

Domain ID domain_id	2a6hM05
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

Domain ID domain_id	2a6hM06
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	2a6hN03
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

Domain ID domain_id	2a6hN04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2a6hN05
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	2a6hN06
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	2a6hN08
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

Domain ID domain_id	2a6hN09
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	280 —

Domain ID domain_id	2a6hO00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

Domain ID domain_id	2a6hP01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1810 —

Domain ID domain_id	2a6hP02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2a6hP03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

▶

Unit-cell length a length_a	239.500 Å
Unit-cell length b length_b	239.500 Å
Unit-cell length c length_c	253.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2680

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin

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

DNA-directed RNA polymerase alpha chain

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 beta chain

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 beta' chain ;

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 omega chain

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 rpoD

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

2a6h__assembly_2__model_1

2a6h__assembly_2__model_1 | I(q)

2a6h__assembly_2__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 60 domains

SCOP 2.08 (20 domains)

CATH v4.4 (40 domains)

7. Citations (1)