1u8r

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions

Method: X-RAY DIFFRACTION

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

Iron-dependent repressor ideR

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 4 DNA 2	mbtA operator DNA × 1 mbtB operator DNA × 1 COBALT (II) ION × 12 SODIUM ION × 4 water × 6	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 4 DNA 2	mbtA operator DNA × 1 mbtB operator DNA × 1 COBALT (II) ION × 12 SODIUM ION × 4 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IDER_MYCTU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–230； UniProt 1–230 Author chain B； PDBConstruct 1–230； UniProt 1–230 Author chain C； PDBConstruct 1–230； UniProt 1–230 Author chain D； PDBConstruct 1–230； UniProt 1–230 Author chain G； PDBConstruct 1–230； UniProt 1–230 Author chain H； PDBConstruct 1–230； UniProt 1–230 Author chain I； PDBConstruct 1–230； UniProt 1–230 Author chain J； PDBConstruct 1–230； UniProt 1–230

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	1u8r
Deposition date deposition_date	2004-08-06
Structure title title	Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions
Keywords keywords	;IdeR, iron-dependent regulator, iron acquisition, siderophores, Mycobacterium tuberculosis, metal-binding protein, Transcription-DNA COMPLEX ;; metal-binding protein,Transcription/DNA
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.

1u8r__assembly_1__model_1

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

Download this curve (.dat)

1u8r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u8r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.81 Å
Rg (electron density)	37.33 Å
Total Rg	37.47 Å
Atom count	8207
Residues	950
Excluded volume	142080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u8r__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1u8r__assembly_2__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	mbtA operator DNA
Molecular weight formula_weight	10112.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,K
Atom count atom_count	16481

CCCTGTTAGCACAGGCTGCCCTAATTTTAGTGG

Entity 2 Entity 2 polymer

Description description	mbtB operator DNA
Molecular weight formula_weight	10188.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,L

CACTAAAATTAGGGCAGCCTGTGCTAACAGGGC

Entity 3 Entity 3 polymer

Description description	Iron-dependent repressor ideR
Molecular weight formula_weight	25281.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,G,H,I,J

MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHVMSEDVERRLVKVLNNPTTSPFGNPIPGLDELGVGPEPGADDANLVRLTELPAGSPVAVVVRQLTEHVQGDIDLITRLKDAGVVPNARVTVETTPGGGVTIVIPGHENVTLPHEMAHAVKVEKV

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d1u8ra1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8ra2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8ra3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1u8rb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8rb2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8rb3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1u8rc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8rc2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8rc3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1u8rd1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8rd2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8rd3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1u8rg1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8rg2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8rg3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1u8rh1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8rh2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8rh3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1u8ri1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8ri2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8ri3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

Domain ID domain_id	d1u8rj1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d1u8rj2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

Domain ID domain_id	d1u8rj3
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.2 — FeoA-like

CATH v4.4 (24 domains)

Domain ID domain_id	1u8rA01
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

Domain ID domain_id	1u8rA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1u8rB01
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

Domain ID domain_id	1u8rB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rB03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1u8rC01
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

Domain ID domain_id	1u8rC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rC03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1u8rD01
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

Domain ID domain_id	1u8rD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rD03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1u8rG01
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

Domain ID domain_id	1u8rG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rG03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1u8rH01
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

Domain ID domain_id	1u8rH02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rH03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1u8rI01
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

Domain ID domain_id	1u8rI02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rI03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

Domain ID domain_id	1u8rJ01
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

Domain ID domain_id	1u8rJ02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

Domain ID domain_id	1u8rJ03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	90 — Ferrous iron transport protein A (FeoA)

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Unit-cell length a length_a	107.959 Å
Unit-cell length b length_b	107.959 Å
Unit-cell length c length_c	215.124 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	24

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	46.750 Å
R factor r_factor	0.2320
R_work r_work	0.2300
R_free r_free	0.2650

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions

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

Iron-dependent repressor ideR

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

1u8r__assembly_1__model_1

1u8r__assembly_1__model_1 | I(q)

1u8r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions

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

Iron-dependent repressor ideR

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

1u8r__assembly_1__model_1

1u8r__assembly_1__model_1 | I(q)

1u8r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)