1nh2

Crystal structure of a yeast TFIIA/TBP/DNA complex

Method: X-RAY DIFFRACTION

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

Transcription initiation factor TFIID

Saccharomyces cerevisiae

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(TPGPTPAP(5IU)PGPTPAPTPAP(5IU)PAPAPAPAPC)-3' × 1 5'-D(GPTPTPTPTPAPTPAPTPAPCPAPTPAPCPA)-3' × 1 Transcription initiation factor IIA large chain × 1 （P32773） Transcription initiation factor IIA large chain × 1 （P32774） Transcription initiation factor IIA small chain × 1 （P32773） water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBP_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 60–239

Transcription initiation factor IIA large chain

Saccharomyces cerevisiae

UniProt P32773

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(TPGPTPAP(5IU)PGPTPAPTPAP(5IU)PAPAPAPAPC)-3' × 1 5'-D(GPTPTPTPTPAPTPAPTPAPCPAPTPAPCPA)-3' × 1 Transcription initiation factor TFIID × 1 （P13393） Transcription initiation factor IIA large chain × 1 （P32774） water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOA1_YEAST
Isoform	—
PDB entities	4, 6
Chains and sequence ranges	Author chain B； PDBConstruct 1–53； UniProt 2–54 Author chain D； PDBConstruct 1–121； UniProt 2–122

Transcription initiation factor IIA large chain

Saccharomyces cerevisiae

UniProt P32774

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(TPGPTPAP(5IU)PGPTPAPTPAP(5IU)PAPAPAPAPC)-3' × 1 5'-D(GPTPTPTPTPAPTPAPTPAPCPAPTPAPCPA)-3' × 1 Transcription initiation factor TFIID × 1 （P13393） Transcription initiation factor IIA large chain × 1 （P32773） Transcription initiation factor IIA small chain × 1 （P32773） water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOA2_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 3–79； UniProt 210–286

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	1nh2
Deposition date deposition_date	2002-12-18
Structure title title	Crystal structure of a yeast TFIIA/TBP/DNA complex
Keywords keywords	TRANSCRIPTION/DNA, 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.

1nh2__assembly_1__model_1

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

Download this curve (.dat)

1nh2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nh2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.54 Å
Rg (electron density)	27.83 Å
Total Rg	28.13 Å
Atom count	3669
Residues	410
Excluded volume	63996 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nh2__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(TPGPTPAP(5IU)PGPTPAPTPAP(5IU)PAPAPAPAPC)-3'
Molecular weight formula_weight	5144.0 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	4204

TGTAUGTATAUAAAAC

Entity 2 Entity 2 polymer

Description description	5'-D(GPTPTPTPTPAPTPAPTPAPCPAPTPAPCPA)-3'
Molecular weight formula_weight	4871.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GTTTTATATACATACA

Entity 3 Entity 3 polymer

Description description	Transcription initiation factor TFIID
Molecular weight formula_weight	20120.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Transcription initiation factor IIA large chain
Molecular weight formula_weight	6135.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTF

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Transcription initiation factor IIA large chain
Molecular weight formula_weight	8915.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSSALLDTDEVGSELDDSDDDYLISEGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Transcription initiation factor IIA small chain
Molecular weight formula_weight	13341.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

AVPGYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSKKSE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
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	477

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1nh2a1
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	d1nh2a2
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	d1nh2b_
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	d1nh2c_
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	d1nh2d1
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	d1nh2d2
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	1nh2A01
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	1nh2A02
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	1nh2B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1nh2C00
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	1nh2D01
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	1nh2D02
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	59.010 Å
Unit-cell length b length_b	92.020 Å
Unit-cell length c length_c	117.017 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	1.900 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2260

Crystal structure of a yeast TFIIA/TBP/DNA complex

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

Transcription initiation factor TFIID

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 large 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 large 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

1nh2__assembly_1__model_1

1nh2__assembly_1__model_1 | I(q)

1nh2__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 (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)