SAXSdb — 9z4e

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

General control transcription factor GCN4

OrganismNot specified

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	DNA (31-MER) × 1 DNA (31-MER) × 1 Replication initiation protein × 1 （P03856） MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCN4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–29； UniProt 226–253 Author chain E； PDBConstruct 1–29； UniProt 226–253 Author chain F； PDBConstruct 1–29； UniProt 226–253

Replication initiation protein

Escherichia coli

UniProt P03856

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	General control transcription factor GCN4 × 3 （P03069） DNA (31-MER) × 1 DNA (31-MER) × 1 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	REPE1_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 13–263； UniProt 1–251

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	9z4e
Deposition date deposition_date	2025-11-10
Last revision last_revision	2026-02-18
Structure title title	Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT and loaded with mutated Bzip region of GCN4 transcription factor
Keywords keywords	Protein-DNA complex, DNA binding protein, Transcription factor, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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.

9z4e__assembly_1__model_1

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

Download this curve (.dat)

9z4e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9z4e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.55 Å
Rg (electron density)	29.08 Å
Total Rg	29.50 Å
Atom count	3166
Residues	328
Excluded volume	51640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9z4e__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 (5)

Entity 1 Entity 1 polymer

Description description	General control transcription factor GCN4
Molecular weight formula_weight	3422.1 kDa
Mutation mutation	residues 251-253 (Uniprot numbering) mutated from KQL to KKQC
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,E
Atom count atom_count	3172

DPAALKRARNTEAARRSRARKLQRMKKQC

Entity 2 Entity 2 polymer

Description description	DNA (31-MER)
Molecular weight formula_weight	9472.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A

CCTGTGACAAATTGCCCTCAGCATGAGTCAT

Entity 3 Entity 3 polymer

Description description	DNA (31-MER)
Molecular weight formula_weight	9592.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

GATGACTCATGCTGAGGGCAATTTGTCACAG

Entity 4 Entity 4 polymer

Description description	Replication initiation protein
Molecular weight formula_weight	30749.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MRGSHHHHHHGSMAETAVINHKKRKNSPRIVQSNDLTEAAYSLSRDQKRMLYLFVDQIRKSDGTLQEHDGICEIHVAKYAEIFGLTSAEASKDIRQALKSFAGKEVVFYRPEEDAGDEKGYESFPWFIKPAHSPSRGLYSVHINPYLIPFFIGLQNRFTQFRLSETKEITNPYAMRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQRMPDFRRRFLQVCVNEINSRTPMRLSYIEKKKGRQTTHIVFSFRDITSMTTG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

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Unit-cell length a length_a	159.036 Å
Unit-cell length b length_b	115.325 Å
Unit-cell length c length_c	72.715 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	3.630 Å
Low-resolution limit resolution_low	65.070 Å
R factor r_factor	0.2512
R_work r_work	0.2473
R_free r_free	0.2853

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT and loaded with mutated Bzip region of GCN4 transcription factor

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

General control transcription factor GCN4

State in the Current Structure

Other States of the Same Protein in the Database

Replication initiation 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

9z4e__assembly_1__model_1

9z4e__assembly_1__model_1 | I(q)

9z4e__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

7. Citations (2)

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CATGAGTCAT and loaded with mutated Bzip region of GCN4 transcription factor

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

General control transcription factor GCN4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Replication initiation 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

9z4e__assembly_1__model_1

9z4e__assembly_1__model_1 | I(q)

9z4e__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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

7. Citations (2)