SAXSdb — 9zum

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

DNA-directed RNA polymerase subunit alpha

Caulobacter vibrioides

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 251–329	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5	Resolution 2.43 Å R-free 0.242
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 251–329	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5	Resolution 2.43 Å R-free 0.242
3	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 251–329	Not recorded	;DNA (5'-D(APAPTPTPAPAPTPTPAPAPTPTPTPTPAPAPTPT)-3') ; × 1 ;DNA (5'-D(APAPTPTPAPAPAPAPTPTPAPAPTPTPAPAPTPT)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5	Resolution 2.43 Å R-free 0.242
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 251–329	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5	Resolution 2.43 Å R-free 0.242
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 251–329	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1-2% PEG 2000 MME, 1 mM Ammonium sulphate, 20 mM sodium acetate pH 5.5	Resolution 2.43 Å R-free 0.242

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZUM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9PFQ The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex Deposited 2025-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric	Chain A 1–338（338 aa） Chain B 1–338（338 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.24 Å
9PFV The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex Deposited 2025-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9PGA The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-didA promoter transcription activation complex Deposited 2025-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 12-meric	Chain A 1–338（338 aa） Chain B 1–338（338 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.98 Å
9PGH The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex Deposited 2025-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–338（338 aa） Chain B 1–338（338 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPOA_CAUVC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–83； UniProt 251–329 Author chain B； PDBConstruct 5–83； UniProt 251–329 Author chain C； PDBConstruct 5–83； UniProt 251–329 Author chain D； PDBConstruct 5–83； UniProt 251–329 Author chain E； PDBConstruct 5–83； UniProt 251–329

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	9zum
Deposition date deposition_date	2025-12-24
最后修订 last_revision	2026-02-25
Structure title title	Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA
Keywords keywords	alphaCTD, RNA polymerase, AT rich DNA, DNA binding, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.31 Å
Radius of gyration Rg (electron density) rg_electron	27.69 Å
Forward intensity I(0) i0	46439200.00
Molecular weight molecular_weight	49324.0 kDa
Excluded volume excluded_volume	60251 Å³
Envelope volume envelope_volume	82905 Å³
Hydration-shell volume shell_volume	25956 Å³
Envelope diameter envelope_diameter	97.0 Å
Shell Rg shell_rg	33.44 Å
Envelope Rg envelope_rg	27.90 Å
Shape Rg shape_rg	27.75 Å
Total Rg total_rg	28.12 Å
Total atoms total_atoms	3426
Residues n_residues	412
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	94.1 Å
Rg (real space) rg_real	27.33 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	4.6440e+07
I(0) uncertainty (real space) i0_real_error	6.2910e+05
Rg (reciprocal space) rg_reciprocal	27.33 Å
I(0) (reciprocal space) i0_reciprocal	46440000.0000
Solution quality estimate total_estimate	0.8785
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.7 Å
Skewness Skewness skewness	0.343
Kurtosis Kurtosis kurtosis	-0.261
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9358000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	9283.6 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	3597

GSHMNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLAGMGLHLGMDVPNWPPENIED

来源 Source

来源生物 organism	Caulobacter vibrioides
NCBI Class编号 ncbi_taxonomy_id	155892
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPTPTPAPAPTPTPAPAPTPTPTPTPAPAPTPT)-3') ;
Molecular weight formula_weight	5502.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

AATTAATTAATTTTAATT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APAPTPTPAPAPAPAPTPTPAPAPTPTPAPAPTPT)-3') ;
Molecular weight formula_weight	5520.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

AATTAAAATTAATTAATT

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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8. Citations (1)

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Unit-cell length a length_a	153.277 Å
Unit-cell length b length_b	153.277 Å
Unit-cell length c length_c	32.078 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	20

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.430 Å
Low-resolution limit resolution_low	42.510 Å
R factor r_factor	0.2130
R_work r_work	0.2107
R_free r_free	0.2416

fit	/app/data/saxs_computation/zu/9zum/9zum.fit
pddf	/app/data/pr_computation/zu/9zum/9zum.pr.out
profile	/app/data/saxs_computation/zu/9zum/9zum.dat

Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)