1pp8

crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element

Method: X-RAY DIFFRACTION

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

39 kDa initiator binding protein

Trichomonas vaginalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	ALPHA-SCS INR × 1 ALPHA-SCS INR × 1	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	ALPHA-SCS INR × 1 ALPHA-SCS INR × 1	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	ALPHA-SCS INR × 1 ALPHA-SCS INR × 1	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	ALPHA-SCS INR × 1 ALPHA-SCS INR × 1	Consistent with all polymers
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	SULFATE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q95VR4_TRIVA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–126； UniProt 1–126 Author chain M； PDBConstruct 1–126； UniProt 1–126 Author chain O； PDBConstruct 1–126； UniProt 1–126 Author chain P； PDBConstruct 1–126； UniProt 1–126 Author chain U； PDBConstruct 1–126； UniProt 1–126 Author chain V； PDBConstruct 1–126； UniProt 1–126

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	1pp8
Deposition date deposition_date	2003-06-16
Structure title title	crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element
Keywords keywords	IBP39, Initiator binding protein, Inr, core promoter, transcription, T. vaginalis, 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.

1pp8__assembly_1__model_1

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

Download this curve (.dat)

1pp8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pp8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.48 Å
Rg (electron density)	16.20 Å
Total Rg	17.14 Å
Atom count	1401
Residues	137
Excluded volume	23415 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pp8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1pp8__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1pp8__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1pp8__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1pp8__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1pp8__assembly_6__model_1`	monomeric （1）	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	ALPHA-SCS INR
Molecular weight formula_weight	3597.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,I,Y,K
Atom count atom_count	7268

GTCACTTCACAT

Entity 2 Entity 2 polymer

Description description	ALPHA-SCS INR
Molecular weight formula_weight	3726.5 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T,R,J,G

CATGTGAAGTGA

Entity 3 Entity 3 polymer

Description description	39 kDa initiator binding protein
Molecular weight formula_weight	15344.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,P,F,V,M,O

MDSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSVFEDPTQNDSPMHHHHHH

Source Source

Source organism organism	Trichomonas vaginalis
NCBI taxonomy ID ncbi_taxonomy_id	5722
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1pp8f_
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.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain

Domain ID domain_id	d1pp8m_
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.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain

Domain ID domain_id	d1pp8o_
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.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain

Domain ID domain_id	d1pp8p_
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.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain

Domain ID domain_id	d1pp8u_
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.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain

Domain ID domain_id	d1pp8v_
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.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1pp8F00
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	1pp8M00
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	1pp8O00
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	1pp8P00
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	1pp8U00
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	1pp8V00
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	292.000 Å
Unit-cell length b length_b	292.000 Å
Unit-cell length c length_c	292.000 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	288

Space group space_group	F 2 3
Space-group number int_tables_number	196
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	146.000 Å
R factor r_factor	0.2690
R_work r_work	0.2690
R_free r_free	0.3110

crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element

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

39 kDa initiator binding protein

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

1pp8__assembly_1__model_1

1pp8__assembly_1__model_1 | I(q)

1pp8__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

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element

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

39 kDa initiator binding protein

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

1pp8__assembly_1__model_1

1pp8__assembly_1__model_1 | I(q)

1pp8__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

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)