1nvp

HUMAN TFIIA/TBP/DNA COMPLEX

Method: X-RAY DIFFRACTION

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

TATA box binding protein

Homo sapiens

UniProt P20226

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	5'-D(GPGPGPGPGPGPGPCPTPAPTPAPAPAPAPGPG)-3' × 1 5'-D(CPCPTPTPTPTPAPTPAPGPCPCPCPCPCPCPC)-3' × 1 Transcription initiation factor IIA alpha chain × 1 （P52655） Transcription initiation factor IIA beta chain × 1 （P52655） Transcription initiation factor IIA gamma chain × 1 （P52657） water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBP_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–181； UniProt 159–339

Transcription initiation factor IIA alpha chain

Homo sapiens

UniProt P52655

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	5'-D(GPGPGPGPGPGPGPCPTPAPTPAPAPAPAPGPG)-3' × 1 5'-D(CPCPTPTPTPTPAPTPAPGPCPCPCPCPCPCPC)-3' × 1 TATA box binding protein × 1 （P20226） Transcription initiation factor IIA gamma chain × 1 （P52657） water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF2AA_HUMAN
Isoform	—
PDB entities	4, 5
Chains and sequence ranges	Author chain B； PDBConstruct 1–57； UniProt 2–58 Author chain C； PDBConstruct 3–76； UniProt 303–376

Transcription initiation factor IIA gamma chain

Homo sapiens

UniProt P52657

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	5'-D(GPGPGPGPGPGPGPCPTPAPTPAPAPAPAPGPG)-3' × 1 5'-D(CPCPTPTPTPTPAPTPAPGPCPCPCPCPCPCPC)-3' × 1 TATA box binding protein × 1 （P20226） Transcription initiation factor IIA alpha chain × 1 （P52655） Transcription initiation factor IIA beta chain × 1 （P52655） water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T2AG_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–108； UniProt 2–109

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	1nvp
Deposition date deposition_date	2003-02-04
Structure title title	HUMAN TFIIA/TBP/DNA COMPLEX
Keywords keywords	TRANSCRIPTION REGULATION, DNA, COMPLEX, 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.

1nvp__assembly_1__model_1

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

Download this curve (.dat)

1nvp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nvp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.46 Å
Rg (electron density)	27.99 Å
Total Rg	28.39 Å
Atom count	3627
Residues	401
Excluded volume	63074 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nvp__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	5'-D(GPGPGPGPGPGPGPCPTPAPTPAPAPAPAPGP*G)-3'
Molecular weight formula_weight	5381.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E
Atom count atom_count	3858

GGGGGGGCTATAAAAGG

Entity 2 Entity 2 polymer

Description description	5'-D(CPCPTPTPTPTPAPTPAPGPCPCPCPCPCPCP*C)-3'
Molecular weight formula_weight	5034.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CCTTTTATAGCCCCCCC

Entity 3 Entity 3 polymer

Description description	TATA box binding protein
Molecular weight formula_weight	20443.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

SGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKTT

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Transcription initiation factor IIA alpha chain
Molecular weight formula_weight	6486.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ANSANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAVDG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Transcription initiation factor IIA beta chain
Molecular weight formula_weight	8687.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSGAEDGQVEEEPLNSEDDVSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Transcription initiation factor IIA gamma chain
Molecular weight formula_weight	12337.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

AYQLYRNTTLGNSLQESLDELIQSQQITPQLALQVLLQFDKAINAALAQRVRNRVNFRGSLNTYRFCDNVWTFVLNDVEFREVTELIKVDKVKIVACDGKNTGSNTTE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1nvpa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1nvpa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1nvpb_
Class class	a — All alpha proteins
Fold Fold fold	a.32 — Transcription factor IIA (TFIIA), alpha-helical domain
Superfamily Superfamily superfamily	a.32.1 — Transcription factor IIA (TFIIA), alpha-helical domain
Family Family family	a.32.1.1 — Transcription factor IIA (TFIIA), alpha-helical domain

Domain ID domain_id	d1nvpc_
Class class	b — All beta proteins
Fold Fold fold	b.56 — Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily Superfamily superfamily	b.56.1 — Transcription factor IIA (TFIIA), beta-barrel domain
Family Family family	b.56.1.1 — Transcription factor IIA (TFIIA), beta-barrel domain

Domain ID domain_id	d1nvpd1
Class class	a — All alpha proteins
Fold Fold fold	a.32 — Transcription factor IIA (TFIIA), alpha-helical domain
Superfamily Superfamily superfamily	a.32.1 — Transcription factor IIA (TFIIA), alpha-helical domain
Family Family family	a.32.1.1 — Transcription factor IIA (TFIIA), alpha-helical domain

Domain ID domain_id	d1nvpd2
Class class	b — All beta proteins
Fold Fold fold	b.56 — Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily Superfamily superfamily	b.56.1 — Transcription factor IIA (TFIIA), beta-barrel domain
Family Family family	b.56.1.1 — Transcription factor IIA (TFIIA), beta-barrel domain

CATH v4.4 (6 domains)

Domain ID domain_id	1nvpA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1nvpA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1nvpB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1nvpC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	18 — TATA box binding Protein, subunit D; domain 2
Homologous superfamily homologous superfamily	10 — Transcription factor IIA (TFIIA), beta-barrel domain

Domain ID domain_id	1nvpD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	190 — Transcription factor IIA gamma subunit, alpha-helical domain

Domain ID domain_id	1nvpD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	18 — TATA box binding Protein, subunit D; domain 2
Homologous superfamily homologous superfamily	10 — Transcription factor IIA (TFIIA), beta-barrel domain

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Unit-cell length a length_a	59.624 Å
Unit-cell length b length_b	90.884 Å
Unit-cell length c length_c	125.256 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	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	39.000 Å
R factor r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2470

HUMAN TFIIA/TBP/DNA COMPLEX

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

TATA box 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

Transcription initiation factor IIA alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcription initiation factor IIA gamma chain

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

1nvp__assembly_1__model_1

1nvp__assembly_1__model_1 | I(q)

1nvp__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 (7)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)