8w8n

Thermus thermophilus initiation transcription complex in the pre-translocated state

Method: X-RAY DIFFRACTION

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

DNA-directed RNA polymerase subunit alpha

OrganismNot specified

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 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q5SKW1） DNA (21-MER) × 1 DNA (27-MER) × 1 ;RNA (5'-D(PPPPP)-R(GPGPU)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 water × 8	Consistent with all polymers

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

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 （Q5SHR6） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q5SKW1） DNA (21-MER) × 1 DNA (27-MER) × 1 ;RNA (5'-D(PPPPP)-R(GPGPU)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 water × 8	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

;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 （Q5SHR6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） RNA polymerase sigma factor SigA × 1 （Q5SKW1） DNA (21-MER) × 1 DNA (27-MER) × 1 ;RNA (5'-D(PPPPP)-R(GPGPU)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 water × 8	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

DNA-directed RNA polymerase subunit omega

OrganismNot specified

UniProt Q8RQE7

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 （Q5SHR6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） RNA polymerase sigma factor SigA × 1 （Q5SKW1） DNA (21-MER) × 1 DNA (27-MER) × 1 ;RNA (5'-D(PPPPP)-R(GPGPU)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 water × 8	Consistent with all polymers

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

RNA polymerase sigma factor SigA

Thermus thermophilus HB8

UniProt Q5SKW1

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 （Q5SHR6） DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q8RQE8） DNA-directed RNA polymerase subunit omega × 1 （Q8RQE7） DNA (21-MER) × 1 DNA (27-MER) × 1 ;RNA (5'-D(PPPPP)-R(GPGPU)-3') ; × 1 MAGNESIUM ION × 6 ZINC ION × 2 water × 8	Consistent with all polymers

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 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	8w8n
Deposition date deposition_date	2023-09-04
Last revision last_revision	2024-07-24
Structure title title	Thermus thermophilus initiation transcription complex in the pre-translocated state
Keywords keywords	Thermus thermophilus, RNA polymerase, pre-translocation, transcription, 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.

8w8n__assembly_1__model_1

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

Download this curve (.dat)

8w8n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8w8n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.83 Å
Rg (electron density)	52.69 Å
Total Rg	52.66 Å
Atom count	28488
Residues	3531
Excluded volume	506420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8w8n__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 (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	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	28636

MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLKE

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVPEDRLQKEMERLYPVEREE

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor SigA
Molecular weight formula_weight	50769.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MGSSHHHHHHSSGLVPRGSHMKKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLTLEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	DNA (21-MER)
Molecular weight formula_weight	6409.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CCTGCATCCGTGACACCAGGG

Entity 7 Entity 7 polymer

Description description	DNA (27-MER)
Molecular weight formula_weight	8421.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

TATAATGGGAGCTGTCACGGATGCAGG

Entity 8 Entity 8 polymer

Description description	;RNA (5'-D(PPPPP)-R(GPGPU)-3') ;
Molecular weight formula_weight	1111.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

GGU

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	6

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	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	140

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Unit-cell length a length_a	184.422 Å
Unit-cell length b length_b	103.704 Å
Unit-cell length c length_c	295.444 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.693 Å
Low-resolution limit resolution_low	48.863 Å
R factor r_factor	0.2133
R_work r_work	0.2124
R_free r_free	0.2599

Thermus thermophilus initiation transcription complex in the pre-translocated state

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

8w8n__assembly_1__model_1

8w8n__assembly_1__model_1 | I(q)

8w8n__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

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 water

7. Citations (1)