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1by4

STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (RETINOIC ACID RECEPTOR RXR-ALPHA)

Homo sapiens

UniProt P19793

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(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') ; × 1 ;DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3') ; × 1 ZINC ION × 4 water × 4 Consistent with all polymers
2 Protein–DNA Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') ; × 1 ;DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3') ; × 1 ZINC ION × 4 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1rxr

1 assemblies

Homodimer
1fby 5tbp 5tbp 6hn6

4 assemblies

Homotetramer
1g1u 1g5y 4n5g 4n8r 5tbp 5zqu 6jno 7cfo

8 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1by4 1by4 1dsz 1fm6 1fm6 1fm9 1k74 1mv9 1mvc 1mzn 1mzn 1r0n

126 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RXRA_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–82； UniProt 128–209 Author chain B； PDBConstruct 1–82； UniProt 128–209 Author chain C； PDBConstruct 1–82； UniProt 128–209 Author chain D； PDBConstruct 1–82； UniProt 128–209

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_id1by4
Deposition date deposition_date1998-10-22
Structure title titleSTRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA
Keywords keywordsRXR, NUCLEAR RECEPTOR, HORMONE RESPONSE ELEMENT, PROTEIN-DNA INTERATIONS, GENE REGULATION-DNA COMPLEX; GENE REGULATION/DNA
Experimental Method methodX-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.

1by4__assembly_1__model_1

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

Download this curve (.dat)

1by4__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1by4__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.16 Å
Rg (electron density)19.97 Å
Total Rg20.68 Å
Atom count1920
Residues191
Excluded volume31961 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1by4__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1by4__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)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1by4a_
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.2 — Nuclear receptor
Domain ID domain_idd1by4b_
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.2 — Nuclear receptor
Domain ID domain_idd1by4c_
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.2 — Nuclear receptor
Domain ID domain_idd1by4d_
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.2 — Nuclear receptor

CATH v4.4 (4 domains)

Domain ID domain_id1by4A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id1by4B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id1by4C00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id1by4D00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
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7. Citations (1)