1hwt

STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN

Method: X-RAY DIFFRACTION

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

PROTEIN (HEME ACTIVATOR PROTEIN)

Saccharomyces cerevisiae

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	;DNA (5'-D(GPCPGPCPTPAPTPTPAPTPCPGPCPTPAPTPTPAPGPC)-3') ; × 1 ;DNA (5'-D(GPCPTPAPAPTPAPGPCPGPAPTPAPAPTPAPGPCPGPC)-3') ; × 1 ZINC ION × 5 water × 4	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(GPCPGPCPTPAPTPTPAPTPCPGPCPTPAPTPTPAPGPC)-3') ; × 1 ;DNA (5'-D(GPCPTPAPAPTPAPGPCPGPAPTPAPAPTPAPGPCPGPC)-3') ; × 1 ZINC ION × 4 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYP1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–81； UniProt 55–135 Author chain D； PDBConstruct 1–81； UniProt 55–135 Author chain G； PDBConstruct 1–81； UniProt 55–135 Author chain H； PDBConstruct 1–81； UniProt 55–135

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	1hwt
Deposition date deposition_date	1998-09-17
Structure title title	STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN
Keywords keywords	TRANSCRIPTION FACTOR, ASYMMETRY, GAL4, COMPLEX ACTIVATOR-DNA, GENE REGULATION-DNA COMPLEX; GENE REGULATION/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.

1hwt__assembly_1__model_1

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

Download this curve (.dat)

1hwt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1hwt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.89 Å
Rg (electron density)	22.67 Å
Total Rg	23.13 Å
Atom count	2010
Residues	184
Excluded volume	33437 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1hwt__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1hwt__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 (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(GPCPGPCPTPAPTPTPAPTPCPGPCPTPAPTPTPAPGPC)-3') ;
Molecular weight formula_weight	6100.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,E
Atom count atom_count	4062

GCGCTATTATCGCTATTAGC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPCPTPAPAPTPAPGPCPGPAPTPAPAPTPAPGPCPGPC)-3') ;
Molecular weight formula_weight	6167.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,F

GCTAATAGCGATAATAGCGC

Entity 3 Entity 3 polymer

Description description	PROTEIN (HEME ACTIVATOR PROTEIN)
Molecular weight formula_weight	9626.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H

RKRNRIPLSCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSKVHSSP

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1hwtc1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1hwtc2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1hwtd1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1hwtd2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1hwtg1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1hwtg2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1hwth1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1hwth2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

CATH v4.4 (8 domains)

Domain ID domain_id	1hwtC01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	1hwtC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	1hwtD01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	1hwtD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	1hwtG01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	1hwtG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	1hwtH01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	1hwtH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

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Unit-cell length a length_a	85.600 Å
Unit-cell length b length_b	85.700 Å
Unit-cell length c length_c	94.000 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	16

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2460
R_work r_work	0.2460
R_free r_free	0.2910

STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN

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

PROTEIN (HEME ACTIVATOR 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

1hwt__assembly_1__model_1

1hwt__assembly_1__model_1 | I(q)

1hwt__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 (5)

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

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

STRUCTURE OF A HAP1/DNA COMPLEX REVEALS DRAMATICALLY ASYMMETRIC DNA BINDING BY A HOMODIMERIC PROTEIN

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

PROTEIN (HEME ACTIVATOR 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

1hwt__assembly_1__model_1

1hwt__assembly_1__model_1 | I(q)

1hwt__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 (5)

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

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)