9pgh

The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex

Method: ELECTRON MICROSCOPY

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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	Protein–DNA	Heteromer	Protein 6 DNA 2	DNA-directed RNA polymerase subunit beta × 1 （Q9AAU2） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9AAU1） DNA-directed RNA polymerase subunit omega × 1 （P58066） RNA polymerase sigma factor RpoD × 1 （P52324） DNA (55-MER)-non template × 1 DNA (43-MER)-template × 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	RPOA_CAUVC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–338； UniProt 1–338 Author chain B； PDBConstruct 1–338； UniProt 1–338

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt Q9AAU2

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 （Q9A8S9） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9AAU1） DNA-directed RNA polymerase subunit omega × 1 （P58066） RNA polymerase sigma factor RpoD × 1 （P52324） DNA (55-MER)-non template × 1 DNA (43-MER)-template × 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	RPOB_CAUVC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1356； UniProt 1–1356

;DNA-directed RNA polymerase subunit beta' ;

OrganismNot specified

UniProt Q9AAU1

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 （Q9A8S9） DNA-directed RNA polymerase subunit beta × 1 （Q9AAU2） DNA-directed RNA polymerase subunit omega × 1 （P58066） RNA polymerase sigma factor RpoD × 1 （P52324） DNA (55-MER)-non template × 1 DNA (43-MER)-template × 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	RPOC_CAUVC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1396； UniProt 1–1396

DNA-directed RNA polymerase subunit omega

OrganismNot specified

UniProt P58066

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 （Q9A8S9） DNA-directed RNA polymerase subunit beta × 1 （Q9AAU2） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9AAU1） RNA polymerase sigma factor RpoD × 1 （P52324） DNA (55-MER)-non template × 1 DNA (43-MER)-template × 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	RPOZ_CAUVC
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–119； UniProt 1–119

RNA polymerase sigma factor RpoD

Caulobacter vibrioides NA1000

UniProt P52324

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 （Q9A8S9） DNA-directed RNA polymerase subunit beta × 1 （Q9AAU2） ;DNA-directed RNA polymerase subunit beta' ; × 1 （Q9AAU1） DNA-directed RNA polymerase subunit omega × 1 （P58066） DNA (55-MER)-non template × 1 DNA (43-MER)-template × 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	RPOD_CAUVC
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–652； UniProt 1–652

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	9pgh
Deposition date deposition_date	2025-07-07
Structure title title	The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex
Keywords keywords	CCNA_03891-CCNA_01149 promoter complex, DriD, Caulobacter, RNA Polymerase, Transcription, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
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.

9pgh__assembly_1__model_1

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

Download this curve (.dat)

9pgh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pgh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.23 Å
Rg (electron density)	52.39 Å
Total Rg	52.53 Å
Atom count	30040
Residues	3815
Excluded volume	527850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pgh__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 (9)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	37315.5 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	A,B
Atom count atom_count	30040

MIERNWNELIRPEKPQIETGADATRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAVTAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGPVTAGQIETPADIEILNPDHVLCTLDDGASVRMEFTVNNGKGYVPADRNRPEDAPIGLIAVDALYSPVKRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAKSADESKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQI

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	151085.6 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

MAQSFTGKKRIRKSFGRIPEAVQMPNLIEVQRSSYEQFLQRETRPGLRRDEGVEAVFKSVFPIKDFNERAVLEYVSYEFEEPKYDVEECIQRDMTFAAPLKVKLRLIVFETEEETGARSVKDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHASGKLLFAARVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTFLYALGMDGEEILTTFYDVVPFEKRSGGWATPYKPERWRGVKPEFPLVDADTGEEVAPAGTKITARQAKKFADGGLKTLLLAPEALTGRYLARDAVNMATGEIYAEAGDELDVTSIQALADQGFSTIDVLDIDHVTVGAYMRNTLRVDKNAIREDALFDIYRVMRPGEPPTVEAAEAMFKSLFFDAERYDLSSVGRVKMNMRLEQDVSDEVRILRKEDVLAVLKVLVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRMERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIESPYRRVKDGKPQDEVVYMSAMEESKHVIAQSNIKVAEGEIVEDLVPGRINGEPTLLQKETVDLMDVSPRQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVQSDAPLVGTGMEAVVARDSGAVVIAKRTGVVEQIDGTRIVIRATEETDPARSGVDIYRMSKFQRSNQSTCINQRPLVKVGDRIVAGDIIADGPSTELGELALGRNALVAFMPWNGYNFEDSILISERIVRDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERALAIERAEIDRLGKDRDDEFAILNRNISGRLKELLIGKVALSGPKGLSRGEITAEGLAQVASGLWWQIALEDEKAMGELESLRRLFDENRKRLDRRFEDKVDKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRILPIEDMPFLADGTHVDVVLNPLGVPSRMNVGQIFETHLGWACANLGKQITNLLEDWQQGGQKQALVERLTEIYGPDEELPDTEEGLVELARNLGKGVPIATPVFDGARMDDIEGHLEMAGVNKSGQSILFDGLTGEQFKRPVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYESIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENS

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	154467.0 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

MNQEVLNIFNPVQAAPTFDQIRISLASPEKIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPTKDYECLCGKYKRMKYKGIICEKCGVEVTLARVRRERMGHIELASPVAHIWFLKSLPSRIAMMLDMPLKDIERVLYFEYYIVTEPGLTPLKQHQLLSEDDYMRAQEEYGDDSFTAEIGAEAIQNLLKAIDLEKEAERLREELSGTVSDMKQKKFSKRLKILEAFQESGNRPEWMVLTVVPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPDIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHECGLPKKMALELFKPFIYARLDAKGLSGTVKQSKRMVEREQPQVWDILEEVIREHPVLLNRAPTLHRLGIQAFEPKLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGRPIIVPSQDIVLGLYYLSVARDGEPGEGKIFADLGEIEAAMDAGVVSLHAKIKARHTEMTPEGVLLRKVIDTTPGRMKIAALLPHHPQIGHRLIEKALTKKEIGNLIDIVYRHCGQKATVIFADKVMGLGFKEAAKAGISFGKDDIIIPVRKTAIVEETRKLAEEYEQQYADGLITKGEKYNKVVDAWAKATDRVADEMMAELQMKHKDENGREKEINAIYMMAHSGARGSQAQMKQLGGMRGLMAKPSGEIIETPIVSNFKEGLTVQEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIIVEEDCGTTKGITLRAVVEGGDVLVSLGSRVLGRFTAEDVKDPGTGELVVPADTYIDENIADAIEAAVVQSVKVRSVLTCEAKIGVCGACYGRDLARGTPVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGTAQVAEQSFFEASNEGTVRVIGPTVVGSDGALVIMSRNTSVSVLVDGKERETYKPPYGARLRVKDGDLVKRGQRLGDWDPYTTPIITEVAGKIRAEDLVDGLSIREEVDEATGIAQRVVADWRTSARGSDLRPAMGVLSEDGSYKRLSNGGEARYLLSAGAILSVADGDEVKPGEVIARIPTEGAKTRDITGGLPRVAELFEARRPKDCAVIAEMDGRVEFGKDYKNKRRIKITPDVDADGNQPEAVEFLIPKGKHIAVHDGDYITKGEYIIDGNPDPHDILRILGVEALANFLVDEIQEVYRLQGVPINDKHIETIVRQMLQKVEILEPGDTGLIKGDHLDKPEFDKEQEKAIARGGRPAVTQPVLLGITKASLQTKSFISAASFQETTRVLTEASVHGKTDTLEGLKENVIVGRLIPAGTGSYLRSLQRVAAKRDEQLAQQREDAMEPLPAEIALSDAE

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	13289.8 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

MARVTVEDCVEKVPNRFALVLLSAHRARGISAGAALMVDRDNDKNPVVALREIADDVIDHEGLKEHLISTLQRVDEHTEAEEEAETLALLADPSHMQMSELELVRALQSDRDGGQEERY

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor RpoD
Molecular weight formula_weight	72770.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSNNSSAETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAMLSEMGVNVVEAEEDAENAEGGEVATRDENTTVIASDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLREVIDLEGTYAAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGPTVSAMEGELREGVMAILDAIASEFEAFRKLQDKLVGSRLKGEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYGISRGEFLKAYFGSELNPTWSEQVKAMGVRWTKFVENDSQSVTDIRSEIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS

Source Source

Source organism organism	Caulobacter vibrioides NA1000
NCBI taxonomy ID ncbi_taxonomy_id	565050
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	DNA (55-MER)-non template
Molecular weight formula_weight	30196.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

CATGCCGCCCGTCATACGACCGTTTCTGTCGCAATGCGCGGACAATCTTCCATCATCGCCCCTGGAGAACCCAAGGACCTTCGATGACCCGCTTCGCCT

Entity 7 Entity 7 polymer

Description description	DNA (43-MER)-template
Molecular weight formula_weight	30894.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

AGGCGAAGCGGGTCATCGAAGGTCCTTGGGTTCTCCAGGGGCGATGATGGAAGATTGTCCGCGCATTGCGACAGAAACGGTCGTATGACGGGCGGCATG

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	1

Entity 9 Entity 9 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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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	—

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

Resolution resolution	3.540 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.54 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	150644

The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex

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 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

9pgh__assembly_1__model_1

9pgh__assembly_1__model_1 | I(q)

9pgh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

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

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

7. Citations (4)