3d1n

Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter

Method: X-RAY DIFFRACTION

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

POU domain, class 6, transcription factor 1

Homo sapiens

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	5'-D(DAPDGPDCPDAPDTPDAPDAPDAPDTPDAPDAPDTPDAPDA)-3' × 1 5'-D(DTPDTPDAPDTPDTPDAPDTPDTPDTPDAPDTPDGPDCPDT)-3' × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	5'-D(DAPDGPDCPDAPDTPDAPDAPDAPDTPDAPDAPDTPDAPDA)-3' × 1 5'-D(DTPDTPDAPDTPDTPDAPDTPDTPDTPDAPDTPDGPDCPDT)-3' × 1 water × 4	Consistent with all polymers
3	Protein–DNA	Homooligomer	Protein 2 DNA 2	5'-D(DAPDGPDCPDAPDTPDAPDAPDAPDTPDAPDAPDTPDAPDA)-3' × 1 5'-D(DTPDTPDAPDTPDTPDAPDTPDTPDTPDAPDTPDGPDCPDT)-3' × 1 water × 4	Consistent with all polymers
4	Protein–DNA	Homooligomer	Protein 2 DNA 2	5'-D(DAPDGPDCPDAPDTPDAPDAPDAPDTPDAPDAPDTPDAPDA)-3' × 1 5'-D(DTPDTPDAPDTPDTPDAPDTPDTPDTPDAPDTPDGPDCPDT)-3' × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PO6F1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–151； UniProt 142–292 Author chain J； PDBConstruct 1–151； UniProt 142–292 Author chain K； PDBConstruct 1–151； UniProt 142–292 Author chain L； PDBConstruct 1–151； UniProt 142–292 Author chain M； PDBConstruct 1–151； UniProt 142–292 Author chain N； PDBConstruct 1–151； UniProt 142–292 Author chain O； PDBConstruct 1–151； UniProt 142–292 Author chain P； PDBConstruct 1–151； UniProt 142–292

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	3d1n
Deposition date deposition_date	2008-05-06
Structure title title	Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter
Keywords keywords	;Protein-DNA complex, Helix-turn-helix (HTH), DNA-binding, Homeobox, Nucleus, Transcription, Transcription regulation, TRANSCRIPTION REGULATOR-DNA COMPLEX ;; TRANSCRIPTION REGULATOR/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.

3d1n__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3d1n__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d1n__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	21.04 Å
Rg (electron density)	20.68 Å
Total Rg	21.37 Å
Atom count	2414
Residues	256
Excluded volume	41145 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d1n__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d1n__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3d1n__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3d1n__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	5'-D(DAPDGPDCPDAPDTPDAPDAPDAPDTPDAPDAPDTPDAPDA)-3'
Molecular weight formula_weight	4304.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,C,E,G
Atom count atom_count	10089

AGCATAAATAATAA

Entity 2 Entity 2 polymer

Description description	5'-D(DTPDTPDAPDTPDTPDAPDTPDTPDTPDAPDTPDGPDCPDT)-3'
Molecular weight formula_weight	4250.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,D,F,H

TTATTATTTATGCT

Entity 3 Entity 3 polymer

Description description	POU domain, class 6, transcription factor 1
Molecular weight formula_weight	17691.5 kDa
Mutation mutation	C186S, C283S, L144M, L172M, I267M
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O,P

INMEEIREFAKNFKIRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKNT

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	97

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6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id	3d1nI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3d1nI02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3d1nJ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3d1nK01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3d1nK02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3d1nL01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3d1nL02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3d1nM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3d1nM02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3d1nN00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3d1nO01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3d1nO02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	3d1nP00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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Unit-cell length a length_a	100.298 Å
Unit-cell length b length_b	112.060 Å
Unit-cell length c length_c	181.504 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	32

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

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	48.910 Å
R factor r_factor	0.2119
R_work r_work	0.2119
R_free r_free	0.2698

Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter

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

POU domain, class 6, transcription factor 1

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

3d1n__assembly_4__model_1

3d1n__assembly_4__model_1 | I(q)

3d1n__assembly_4__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 water

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)

Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter

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

POU domain, class 6, transcription factor 1

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

3d1n__assembly_4__model_1

3d1n__assembly_4__model_1 | I(q)

3d1n__assembly_4__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 water

6. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. Citations (1)