1rp3

Cocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM

Method: X-RAY DIFFRACTION

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

RNA polymerase sigma factor SIGMA-28 (FliA)

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O67268_AQUAE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 4–239； UniProt 1–236 Author chain C； PDBConstruct 4–239； UniProt 1–236 Author chain E； PDBConstruct 4–239； UniProt 1–236 Author chain G； PDBConstruct 4–239； UniProt 1–236 Author chain B； PDBConstruct 1–88； UniProt 43–100 Author chain D； PDBConstruct 1–88； UniProt 43–100 Author chain F； PDBConstruct 1–88； UniProt 43–100 Author chain H； PDBConstruct 1–88； UniProt 43–100

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	1rp3
Deposition date deposition_date	2003-12-02
Structure title title	Cocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM
Keywords keywords	TRANSCRIPTION, SIGMA FACTOR; 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.

1rp3__assembly_1__model_1

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

Download this curve (.dat)

1rp3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rp3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.56 Å
Rg (electron density)	21.31 Å
Total Rg	22.24 Å
Atom count	2338
Residues	312
Excluded volume	42096 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rp3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rp3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1rp3__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1rp3__assembly_4__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	RNA polymerase sigma factor SIGMA-28 (FliA)
Molecular weight formula_weight	27735.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	9110

GSHMKNPYSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALERLREMLSNPL

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	anti sigma factor FlgM
Molecular weight formula_weight	10257.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MVNRIELSRLIGLLLETEKRKNTEQKESGTNKIEDKVTLSKIAQELSKNDVEEKDLEKKVKELKEKIEKGEYEVSDEKVVKGLIEFFT

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

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6. Fold Classification (SCOP + CATH) 33 domains

SCOP 2.08 (17 domains)

Domain ID domain_id	d1rp3a1
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.4.13.1 — Sigma3 domain

Domain ID domain_id	d1rp3a2
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

Domain ID domain_id	d1rp3a3
Class class	a — All alpha proteins
Fold Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

Domain ID domain_id	d1rp3a4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1rp3b_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.11 — Anti-sigma factor FlgM
Family Family family	a.137.11.1 — Anti-sigma factor FlgM

Domain ID domain_id	d1rp3c1
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.4.13.1 — Sigma3 domain

Domain ID domain_id	d1rp3c2
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

Domain ID domain_id	d1rp3c3
Class class	a — All alpha proteins
Fold Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

Domain ID domain_id	d1rp3d_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.11 — Anti-sigma factor FlgM
Family Family family	a.137.11.1 — Anti-sigma factor FlgM

Domain ID domain_id	d1rp3e1
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.4.13.1 — Sigma3 domain

Domain ID domain_id	d1rp3e2
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

Domain ID domain_id	d1rp3e3
Class class	a — All alpha proteins
Fold Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

Domain ID domain_id	d1rp3f_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.11 — Anti-sigma factor FlgM
Family Family family	a.137.11.1 — Anti-sigma factor FlgM

Domain ID domain_id	d1rp3g1
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.4.13.1 — Sigma3 domain

Domain ID domain_id	d1rp3g2
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

Domain ID domain_id	d1rp3g3
Class class	a — All alpha proteins
Fold Fold fold	a.177 — Sigma2 domain of RNA polymerase sigma factors
Superfamily Superfamily superfamily	a.177.1 — Sigma2 domain of RNA polymerase sigma factors
Family Family family	a.177.1.1 — Sigma2 domain of RNA polymerase sigma factors

Domain ID domain_id	d1rp3h_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.11 — Anti-sigma factor FlgM
Family Family family	a.137.11.1 — Anti-sigma factor FlgM

CATH v4.4 (16 domains)

Domain ID domain_id	1rp3A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

Domain ID domain_id	1rp3A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	160 — PhyR, sigma-like (SL) domain

Domain ID domain_id	1rp3B01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	1rp3B02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	30 — Anti-sigma-28 factor FlgM

Domain ID domain_id	1rp3C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

Domain ID domain_id	1rp3C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	160 — PhyR, sigma-like (SL) domain

Domain ID domain_id	1rp3D01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	1rp3D02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	30 — Anti-sigma-28 factor FlgM

Domain ID domain_id	1rp3E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

Domain ID domain_id	1rp3E02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	160 — PhyR, sigma-like (SL) domain

Domain ID domain_id	1rp3F01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	1rp3F02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	30 — Anti-sigma-28 factor FlgM

Domain ID domain_id	1rp3G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

Domain ID domain_id	1rp3G02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	160 — PhyR, sigma-like (SL) domain

Domain ID domain_id	1rp3H01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	1rp3H02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	30 — Anti-sigma-28 factor FlgM

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Unit-cell length a length_a	76.388 Å
Unit-cell length b length_b	119.666 Å
Unit-cell length c length_c	100.056 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.920 Å
R factor r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2620

Cocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM

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

RNA polymerase sigma factor SIGMA-28 (FliA)

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

1rp3__assembly_1__model_1

1rp3__assembly_1__model_1 | I(q)

1rp3__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 33 domains

SCOP 2.08 (17 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Cocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM

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

RNA polymerase sigma factor SIGMA-28 (FliA)

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

1rp3__assembly_1__model_1

1rp3__assembly_1__model_1 | I(q)

1rp3__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 33 domains

SCOP 2.08 (17 domains)

CATH v4.4 (16 domains)

7. Citations (1)