1h0m

Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA

Method: X-RAY DIFFRACTION

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

Transcriptional activator protein TraR

Rhizobium radiobacter

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;5'-D(APTPGPTPGPCPAPGPAPTP CPTPGPCPAPCPAPT)-3' ; × 2 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE × 2 water × 3	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	;5'-D(APTPGPTPGPCPAPGPAPTP CPTPGPCPAPCPAPT)-3' ; × 2 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRAR_RHIRD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 1–234 Author chain B； PDBConstruct 1–234； UniProt 1–234 Author chain C； PDBConstruct 1–234； UniProt 1–234 Author chain D； PDBConstruct 1–234； UniProt 1–234

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	1h0m
Deposition date deposition_date	2002-06-25
Structure title title	Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA
Keywords keywords	;TRANSCRIPTION/DNA, LUXR-TYPE PROTEIN, QUORUM SENSING, TRANSCRIPTIONAL REGULATOR, DNA-BINDING PROTEIN, HOMOSERINE LACTONE, TRAR, TRANSCRIPTION-DNA complex ;; 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.

1h0m__assembly_1__model_1

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

Download this curve (.dat)

1h0m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1h0m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.00 Å
Rg (electron density)	26.55 Å
Total Rg	27.27 Å
Atom count	4476
Residues	484
Excluded volume	77512 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1h0m__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1h0m__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	Transcriptional activator protein TraR
Molecular weight formula_weight	27060.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9013

MQHWLDKLTDLAAIEGDECILKTGLADIADHFGFTGYAYLHIQHRHITAVTNYHRQWQSTYFDKKFEALDPVVKRARSRKHIFTWSGEHERPTLSKDERAFYDHASDFGIRSGITIPIKTANGFMSMFTMASDKPVIDLDREIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI

Source Source

Source organism organism	Rhizobium radiobacter
Common name common_name	Agrobacterium tumefaciens
NCBI taxonomy ID ncbi_taxonomy_id	358
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	;5'-D(APTPGPTPGPCPAPGPAPTP CPTPGPCPAPCPAPT)-3' ;
Molecular weight formula_weight	5515.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F,G,H

ATGTGCAGATCTGCACAT

Entity 3 Entity 3 non-polymer

Description description	3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
Molecular weight formula_weight	241.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1h0ma1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

Domain ID domain_id	d1h0ma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
Family Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

Domain ID domain_id	d1h0mb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

Domain ID domain_id	d1h0mb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
Family Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

Domain ID domain_id	d1h0mc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

Domain ID domain_id	d1h0mc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
Family Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

Domain ID domain_id	d1h0md1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family family	a.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)

Domain ID domain_id	d1h0md2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.5 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
Family Family family	d.110.5.1 — Pheromone-binding domain of LuxR-like quorum-sensing transcription factors

CATH v4.4 (8 domains)

Domain ID domain_id	1h0mA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	1h0mA02
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	1h0mB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	1h0mB02
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	1h0mC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	1h0mC02
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	1h0mD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	1h0mD02
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	66.993 Å
Unit-cell length b length_b	94.678 Å
Unit-cell length c length_c	209.669 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2330
R_free r_free	0.2850

Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA

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

Transcriptional activator protein TraR

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

1h0m__assembly_1__model_1

1h0m__assembly_1__model_1 | I(q)

1h0m__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)

Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA

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

Transcriptional activator protein TraR

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

1h0m__assembly_1__model_1

1h0m__assembly_1__model_1 | I(q)

1h0m__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (2)