SAXSdb — 2p7v

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

Regulator of sigma D

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	RNA polymerase sigma factor rpoD × 1 （P00579） MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	RNA polymerase sigma factor rpoD × 2 （P00579） MAGNESIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RSD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158

RNA polymerase sigma factor rpoD

Escherichia coli

UniProt P00579

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Regulator of sigma D × 1 （P0AFX4） MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Regulator of sigma D × 2 （P0AFX4） MAGNESIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOD_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–68； UniProt 546–613

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	2p7v
Deposition date deposition_date	2007-03-20
Structure title title	Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4
Keywords keywords	;Rsd, sigma 70, Regulator of sigma 70, sigma 70 domain 4, transcription, regulation, Helix-turn-helix, Rsd-sigma 70 complex, sigma factor, Escherichia coli Rsd-sigma 70 complex, E. coli Rsd-sigma 70 complex ;; TRANSCRIPTION
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.

2p7v__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2p7v__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p7v__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.91 Å
Rg (electron density)	23.76 Å
Total Rg	24.59 Å
Atom count	3541
Residues	438
Excluded volume	62864 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p7v__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2p7v__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Regulator of sigma D
Molecular weight formula_weight	18266.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1865

MLNQLDNLTERVRGSNKLVDRWLHVRKHLLVAYYNLVGIKPGKESYMRLNEKALDDFCQSLVDYLSAGHFSIYERILHKLEGNGQLARAAKIWPQLEANTQQIMDYYDSSLETAIDHDNYLEFQQVLSDIGEALEARFVLEDKLILLVLDAARVKHPA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RNA polymerase sigma factor rpoD
Molecular weight formula_weight	7977.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2p7vb_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.13 — Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family Family family	a.4.13.2 — Sigma4 domain

CATH v4.4 (2 domains)

Domain ID domain_id	2p7vA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1370 — Regulator of RNA polymerase sigma(70) subunit, domain 4

Domain ID domain_id	2p7vB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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Unit-cell length a length_a	84.111 Å
Unit-cell length b length_b	84.111 Å
Unit-cell length c length_c	84.219 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2400
R_work r_work	0.2390
R_free r_free	0.2730

Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4

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

Regulator of sigma D

State in the Current Structure

Other States of the Same Protein in the Database

RNA polymerase sigma factor rpoD

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2p7v__assembly_2__model_1

2p7v__assembly_2__model_1 | I(q)

2p7v__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4

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

Regulator of sigma D

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

2p7v__assembly_2__model_1

2p7v__assembly_2__model_1 | I(q)

2p7v__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)