6j9f

Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with the bacteriophage protein P7

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase subunit alpha

Xanthomonas oryzae pv. oryzae PXO99A

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 （Q2NZX8） ;DNA-directed RNA polymerase subunit beta' ; × 1 （B2SQQ2） DNA-directed RNA polymerase subunit omega × 1 （A0A0U4VN94） DNA (29-MER) × 1 DNA (29-MER) × 1 ;RNA (5'-R(PAPGPCPGPGPAPGPAPGPGPUPA)-3') ; × 1 45L × 1 （Q8LTJ5） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_XANOP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–346； UniProt 1–332 Author chain B； PDBConstruct 15–346； UniProt 1–332

DNA-directed RNA polymerase subunit beta

Xanthomonas oryzae pv. oryzae MAFF 311018

UniProt Q2NZX8

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 （B2SQT4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （B2SQQ2） DNA-directed RNA polymerase subunit omega × 1 （A0A0U4VN94） DNA (29-MER) × 1 DNA (29-MER) × 1 ;RNA (5'-R(PAPGPCPGPGPAPGPAPGPGPUPA)-3') ; × 1 45L × 1 （Q8LTJ5） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_XANOM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1383； UniProt 1–1383

;DNA-directed RNA polymerase subunit beta' ;

Xanthomonas oryzae pv. oryzae PXO99A

UniProt B2SQQ2

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 （B2SQT4） DNA-directed RNA polymerase subunit beta × 1 （Q2NZX8） DNA-directed RNA polymerase subunit omega × 1 （A0A0U4VN94） DNA (29-MER) × 1 DNA (29-MER) × 1 ;RNA (5'-R(PAPGPCPGPGPAPGPAPGPGPUPA)-3') ; × 1 45L × 1 （Q8LTJ5） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_XANOP
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1405； UniProt 1–1405

DNA-directed RNA polymerase subunit omega

Xanthomonas oryzae pv. oryzae

UniProt A0A0U4VN94

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 （B2SQT4） DNA-directed RNA polymerase subunit beta × 1 （Q2NZX8） ;DNA-directed RNA polymerase subunit beta' ; × 1 （B2SQQ2） DNA (29-MER) × 1 DNA (29-MER) × 1 ;RNA (5'-R(PAPGPCPGPGPAPGPAPGPGPUPA)-3') ; × 1 45L × 1 （Q8LTJ5） MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0U4VN94_XANOO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–99； UniProt 1–99

45L

Xanthomonas virus Xp10

UniProt Q8LTJ5

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 （B2SQT4） DNA-directed RNA polymerase subunit beta × 1 （Q2NZX8） ;DNA-directed RNA polymerase subunit beta' ; × 1 （B2SQQ2） DNA-directed RNA polymerase subunit omega × 1 （A0A0U4VN94） DNA (29-MER) × 1 DNA (29-MER) × 1 ;RNA (5'-R(PAPGPCPGPGPAPGPAPGPGPUPA)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8LTJ5_9CAUD
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain J； PDBConstruct 5–77； UniProt 1–73

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	6j9f
Deposition date deposition_date	2019-01-22
Structure title title	Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with the bacteriophage protein P7
Keywords keywords	;RNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, Xanthomonos oryzae, Xp10, transcription ;; TRANSCRIPTION
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.

6j9f__assembly_1__model_1

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

Download this curve (.dat)

6j9f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6j9f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.46 Å
Rg (electron density)	45.97 Å
Total Rg	46.13 Å
Atom count	23658
Residues	3122
Excluded volume	414400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6j9f__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	38030.2 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	23658

MGSSHHHHHHSQDPMTVTANQVLRPRGPQIERLTDNRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLDVLLNLKDVAIRMHSGDSATLSLSKQGPGTVTAADIRTDHNVEIINGDHVICHLTKDTALNMRLKIERGFGYQPAAARRRPDEETRTIGRLMLDASFSPVRRVAYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAASGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLAQRGLALGMKLENWPPAGVAQHGMLG

Source Source

Source organism organism	Xanthomonas oryzae pv. oryzae PXO99A
NCBI taxonomy ID ncbi_taxonomy_id	360094
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	154471.7 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

MTSYSFTEKKRIRKDFGKQRSILEVPFLLAIQVDSYREFLQEDVESTKRKDLGLHAALKSVFPISSYSGNAALEYVGYKLGQPVFDERECRQRGMSYGAPLRVTVRLVIYDRESSTKAIKYVKEQEVYLGEIPLMTGNGTFIVNGTERVIVSQLHRSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDALFTRIDRRRKLPVSILLRALGYNNEEMLAEFFEINTFHINPDEGVQLELVPERLRGETLNFDLADGDKVIVEAGKRITARHVKQLEAAGVAALAVPDDYLVGRILSHDVVDGSTGELLANANDEISEDQLTAFRKAGVDAVGTLWVNDLDRGPYLSNTLRIDPTKTQLEALVEIYRMMRPGEPPTKEAAQNLFHNLFFTFERYDLSTVGRMKFNRRVGRKDVLGESVLYDKKYFAERNDEESKRLVAEHTDTSDILEVIKVLTEIRNGRGVVDDIDHLGNRRVRSVGEMAENVFRVGLVRVERAVKERLSMAESEGLTPQELINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEVTHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCTIETPEGPNIGLINSLAVFARTNQYGFLETPYRKVLDGKVSDDVEYLSAIEENEYVIAQANALTDAKNMLTEQFVPCRFQGESLLKPPSEVHFMDVSPMQTVSVAAALVPFLEHDDANRALMGANMQRQAVPTLRSQKPLVGTGIERAVARDSGVTVNALRGGVIEQIDAARIVVKVNEAEIGGGTDAGVDIYNLIKYTRSNQNTCINQRPLVNVGDVIARGDVLADGPSTDIGELALGQNMLIAFMPWNGYNFEDSILLSERVVEEDRYTTIHIEELTCVARDTKLGPEEISADIPNVSEQALNRLDESGVVYIGAEVRAGDIMVGKVTPKGESQLTPEEKLLRAIFGEKASDVKDSSLRVPPGMDGTVIDVQVFTRDGIEKDKRARQIEENEIKRVKKDFDDQFRILEAAIYARLRSQIVGKVANGGANLKKGDSVTDAYLDGLKKSDWFQLRMKDEDAADAIERAQKQIQAHEKEFEARFADKRGKITQGDDLAPGVLKMVKVFLAVKRRIQPGDKMAGRHGNKGVVSNVVPVEDMPYMATGESVDIVLNPLGVPSRMNIGQILEVHLGWAAKGLGRKIQRMLEAQAAVSELRKFLDDIYNHDNAINAQRVDLSQFSDEELLNLGKNLIDGVPMATPVFDGASEAEIKRMLELADLPQSGQTQLYDGRTGEAFDRKTTVGYMHYLKLNHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVQGRNQMYKNIVDGEHEMVAGMPESFNVLVKEIRSLAIHMELEE

Source Source

Source organism organism	Xanthomonas oryzae pv. oryzae MAFF 311018
NCBI taxonomy ID ncbi_taxonomy_id	342109
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	155444.6 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

MKDLLNLFNQQRQTLDFDAIKIALASPDLIRSWSYGEVKKPETINYRTFKPERDGLFCAAIFGPIKDYECLCGKYKRMKHRGVVCEKCGTEVTLAKVRRERMGHIDLASPVAHIWFLKSLPSRIGLMLDMTLRDIERVLYFEAYVVTEPGLTPLERRQLLTEEQYLTARQEYNDDFDAAMGAEAVYELLRTIDLQSEMTRLREEIASTGSETKLKRLTKRIKLIEAFLESGNRPEWMVMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLRRLLELNAPDIIVRNEKRMLQESVDALLDNGRRGRAITGTNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLKLHQCGLPKKMALELFKPFVFAKLQRRGLATTIKAAKKLVEREEAEVWDILEEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMSRALENKKGEGMVFANTSEVKRAYDNRVVELHAKVKVRITQVDVDAVDGKRTSGTSIVDTTVGRALLSEILPEGLPFQLANTEMTKKNISRLINSSYRLLGLKDTVVFADKLMYTGYAYATRAGVSIGIDDMLIPDEKKGILTEAEAEVLEIQEQYQSGLVTAGERYNKVVDIWSRTSERIAKAMMDTIGTEKVENAKGETIDQKSMNSLYIMADSGARGSQAQIRQLAGMRGLMARPDGSIIETPIKANFREGLNVQEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEIDCGTTEGLIMTPIVEGGDVVEPLKERVLGRVVAEDVYLPGNDEEPIVTRNTLLDEAWVAKLEDASVQSVKVRSTISCESSFGVCARCYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAVDNITVKTTGSVKFNNLKSVAHASGSLVAVSRSGELSVLDGHGRERERYKLPYGATITAKDGDAVKAGQSVANWDPHNHPIVSEVAGFIRFIDFVDGVTVIEKTDELTGLASREITDPKRRGAHAKELRPIVRIVDGKGNDLTIPNTDLPAQYLLPPRSIVNLQDGAAVGVGDVVAKIPQEASKTRDITGGLPRVADLFEARKPKDPAILAERSGIISFGKDTKGKQRLIIKDTDGSEHEELIPKYRQIIVFEGEHVTKGETVVDGEPSPQDILRLLGVEPLAAYLVKEIQDVYRLQGVKINDKHIEVITRQMLRKVEIVDQGNSKFLNGEQVERQRVIEENARLVKRNELPAKYDPVLLGITKASLATESFISAASFQETTRVLTEAAVRGTRDNLRGLKENVIVGRLIPAGTGLAYHAGRRKASGLTDSEMETLSGKPAGAEPVAALADAGADEE

Source Source

Source organism organism	Xanthomonas oryzae pv. oryzae PXO99A
NCBI taxonomy ID ncbi_taxonomy_id	360094
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	11112.5 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

MARITVEDCLEVVNNRFELVMMASKRARQLANGVQPLIENAAASDKPTVMALREIAARRIDNALIDEVEKAERERAEREALEWAAAEVVADEDMSKNDD

Source Source

Source organism organism	Xanthomonas oryzae pv. oryzae
NCBI taxonomy ID ncbi_taxonomy_id	64187
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	DNA (29-MER)
Molecular weight formula_weight	8813.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

GGGTATTCGCCGTGTACCTCTCCTAGCCC

Entity 6 Entity 6 polymer

Description description	DNA (29-MER)
Molecular weight formula_weight	8840.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

GGGCTACCTCTCCATGACGGCGAATACCC

Entity 7 Entity 7 polymer

Description description	;RNA (5'-R(PAPGPCPGPGPAPGPAPGPGPUPA)-3') ;
Molecular weight formula_weight	6510.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

GCAUUCAAAGCGGAGAGGUA

Entity 8 Entity 8 polymer

Description description	45L
Molecular weight formula_weight	8519.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

GAMAMNEFTQISGYVNAFGSQRGSVLTVKVENDEGWTLVEEDFDRADYGSDPEFVAEVSSYLKRNGGIKDLTKVLTR

Source Source

Source organism organism	Xanthomonas virus Xp10
NCBI taxonomy ID ncbi_taxonomy_id	232237
Host organism host_organism	Escherichia coli BL21(DE3)

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

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6j9fA01
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	6j9fA02
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	6j9fB01
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	6j9fB02
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	6j9fD01
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	6j9fD02
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	6j9fE00
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	6j9fJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	560 —

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with the bacteriophage protein P7

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

45L

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

6j9f__assembly_1__model_1

6j9f__assembly_1__model_1 | I(q)

6j9f__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)