1utd

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats

Method: X-RAY DIFFRACTION

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

TRANSCRIPTION ATTENUATION PROTEIN MTRB

BACILLUS STEAROTHERMOPHILUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 11	TRYPTOPHAN × 11 water × 11	Consistent with protein count
2	Protein–RNA	Homooligomer	Protein 11 RNA 11	5'-R(GPUPUPUPGPAP)-3' × 11 TRYPTOPHAN × 11 water × 22	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRB_BACST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–74； UniProt 1–74 Author chain B； PDBConstruct 1–74； UniProt 1–74 Author chain C； PDBConstruct 1–74； UniProt 1–74 Author chain D； PDBConstruct 1–74； UniProt 1–74 Author chain E； PDBConstruct 1–74； UniProt 1–74 Author chain F； PDBConstruct 1–74； UniProt 1–74 Author chain G； PDBConstruct 1–74； UniProt 1–74 Author chain H； PDBConstruct 1–74； UniProt 1–74 Author chain I； PDBConstruct 1–74； UniProt 1–74 Author chain J； PDBConstruct 1–74； UniProt 1–74 Author chain K； PDBConstruct 1–74； UniProt 1–74 Author chain L； PDBConstruct 1–74； UniProt 1–74 Author chain M； PDBConstruct 1–74； UniProt 1–74 Author chain N； PDBConstruct 1–74； UniProt 1–74 Author chain O； PDBConstruct 1–74； UniProt 1–74 Author chain P； PDBConstruct 1–74； UniProt 1–74 Author chain Q； PDBConstruct 1–74； UniProt 1–74 Author chain R； PDBConstruct 1–74； UniProt 1–74 Author chain S； PDBConstruct 1–74； UniProt 1–74 Author chain T； PDBConstruct 1–74； UniProt 1–74 Author chain U； PDBConstruct 1–74； UniProt 1–74 Author chain V； PDBConstruct 1–74； UniProt 1–74

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	1utd
Deposition date deposition_date	2003-12-08
Structure title title	The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats
Keywords keywords	RNA BINDING PROTEIN, TRANSCRIPTION REGULATION, RNA-BINDING, TRP RNA TRANSCRIPTION ATTENUATION, RNA-BINDING PROTEIN; RNA BINDING PROTEIN
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.

1utd__assembly_1__model_1

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

Download this curve (.dat)

1utd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1utd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.47 Å
Rg (electron density)	29.45 Å
Total Rg	30.41 Å
Atom count	6163
Residues	774
Excluded volume	108880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1utd__assembly_1__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1utd__assembly_2__model_1`	22-meric （22）	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	5'-R(GPUPUPUPGPAP)-3'
Molecular weight formula_weight	1893.2 kDa
Source method src_method	syn
Copy count entity_count	11

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	0,1,2,3,4,5,6,7,8,9,Z
Atom count atom_count	14124

GUUUGA

Entity 2 Entity 2 polymer

Description description	TRANSCRIPTION ATTENUATION PROTEIN MTRB
Molecular weight formula_weight	8257.4 kDa
Source method src_method	man
Copy count entity_count	22

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V

MYTNSDFVVIKALEDGVNVIGLTRGADTRFHHSEKLDKGEVLIAQFTEHTSAIKVRGKAYIQTRHGVIESEGKK

Source Source

Source organism organism	BACILLUS STEAROTHERMOPHILUS
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	983

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6. Fold Classification (SCOP + CATH) 44 domains

SCOP 2.08 (22 domains)

Domain ID domain_id	d1utda_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdc_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdd_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utde_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdf_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdg_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdh_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdi_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdj_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdk_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdl_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdm_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdn_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdo_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdp_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdq_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdr_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utds_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdt_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdu_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

Domain ID domain_id	d1utdv_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.5 — TRAP-like
Family Family family	b.82.5.1 — Trp RNA-binding attenuation protein (TRAP)

CATH v4.4 (22 domains)

Domain ID domain_id	1utdA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdM00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdN00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdO00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdP00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdQ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdR00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdS00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdT00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdU00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

Domain ID domain_id	1utdV00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	50 — TRAP-like

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Unit-cell length a length_a	115.110 Å
Unit-cell length b length_b	134.230 Å
Unit-cell length c length_c	119.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	88

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1700
R_work r_work	0.1690
R_free r_free	0.2280

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats

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

TRANSCRIPTION ATTENUATION PROTEIN MTRB

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

1utd__assembly_1__model_1

1utd__assembly_1__model_1 | I(q)

1utd__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

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) 44 domains

SCOP 2.08 (22 domains)

CATH v4.4 (22 domains)

7. Citations (3)

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats

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

TRANSCRIPTION ATTENUATION PROTEIN MTRB

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

1utd__assembly_1__model_1

1utd__assembly_1__model_1 | I(q)

1utd__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

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) 44 domains

SCOP 2.08 (22 domains)

CATH v4.4 (22 domains)

7. Citations (3)