5x22

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and CMPcPP

Method: X-RAY DIFFRACTION

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

DNA-directed RNA polymerase subunit alpha

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_THETH
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 subunit beta

OrganismNot specified

UniProt Q8RQE9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers

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 subunit beta' ;

OrganismNot specified

UniProt Q8RQE8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers

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

DNA-directed RNA polymerase subunit omega

OrganismNot specified

UniProt Q72ID6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） RNA polymerase sigma factor SigA × 1 （Q72L95） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOZ_THET2
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 SigA

Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)

UniProt Q72L95

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （Q9Z9H6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q72ID6） promoter DNA template strand × 1 promoter DNA nontemplate strand × 1 ;RNA (5'-R(GPA)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIGA_THET2
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 21–443； UniProt 1–423 Author chain P； PDBConstruct 21–443； 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	5x22
Deposition date deposition_date	2017-01-29
Structure title title	Crystal structure of Thermus thermophilus transcription initiation complex with GpA and CMPcPP
Keywords keywords	Transcription, RNA polymerase, primer-dependent initiation, TRANSFERASE-DNA complex; TRANSFERASE/DNA
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.

5x22__assembly_1__model_1

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

Download this curve (.dat)

5x22__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5x22__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.75 Å
Rg (electron density)	52.65 Å
Total Rg	52.61 Å
Atom count	28072
Residues	3473
Excluded volume	498540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5x22__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5x22__assembly_2__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 (11)

Entity 1 Entity 1 polymer

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

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,K,L
Atom count atom_count	56863

MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLKE

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Thermus thermophilus

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
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 subunit beta' ;
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	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	11533.3 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	E,O

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVPEDRLQKEMERLYPVEREE

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor SigA
Molecular weight formula_weight	50739.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGSSHHHHHHSSGLVPRGSHMKKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

Source Source

Source organism organism	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
NCBI taxonomy ID ncbi_taxonomy_id	262724
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	promoter DNA template strand
Molecular weight formula_weight	6480.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G,Q

CCTGCATCCGTGAGTCGAGGG

Entity 7 Entity 7 polymer

Description description	promoter DNA nontemplate strand
Molecular weight formula_weight	8421.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H,R

TATAATGGGAGCTGTCACGGATGCAGG

Entity 8 Entity 8 polymer

Description description	;RNA (5'-R(GPA)-3') ;
Molecular weight formula_weight	629.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I,S

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	12

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

Description description	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
Molecular weight formula_weight	481.2 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id	5x22A01
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	5x22A02
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	5x22B01
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	5x22B02
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	5x22C01
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	5x22C02
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	5x22E00
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	5x22K01
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	5x22K02
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	5x22L01
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	5x22L02
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	5x22M01
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	5x22M02
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	5x22N01
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	5x22O00
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

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Unit-cell length a length_a	186.410 Å
Unit-cell length b length_b	104.320 Å
Unit-cell length c length_c	297.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.350 Å
Low-resolution limit resolution_low	49.022 Å
R factor r_factor	0.2100
R_work r_work	0.2079
R_free r_free	0.2503

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and CMPcPP

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

5x22__assembly_1__model_1

5x22__assembly_1__model_1 | I(q)

5x22__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

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

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

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)