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1u3e

DNA binding and cleavage by the HNH homing endonuclease I-HmuI

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

HNH homing endonuclease

Bacillus phage SPO1

UniProt P34081

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 3 36-MER × 1 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3' × 1 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3' × 1 STRONTIUM ION × 4 1,2-ETHANEDIOL × 7 MANGANESE (II) ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1u3e

1 assemblies

View Construct and Data Evidence
UniProt name YG31_BPSP1
Isoform —
PDB entities 4
Chains and sequence ranges Author chain M； PDBConstruct 1–174； UniProt 1–174

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_id1u3e
Deposition date deposition_date2004-07-21
Structure title titleDNA binding and cleavage by the HNH homing endonuclease I-HmuI
Keywords keywordsHNH catalytic motif, Helix-turn-helix DNA binding domain, protein-DNA complex, DNA binding protein-DNA COMPLEX; DNA binding protein/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.

1u3e__assembly_1__model_1

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

Download this curve (.dat)

1u3e__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.

1u3e__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）31.81 Å
Rg (electron density)31.73 Å
Total Rg32.06 Å
Atom count2905
Residues246
Excluded volume47250 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1u3e__assembly_1__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 (9)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1u3em1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.4 — His-Me finger endonucleases
Superfamily Superfamily superfamilyd.4.1 — His-Me finger endonucleases
Family Family familyd.4.1.3 — Intron-encoded homing endonucleases
Domain ID domain_idd1u3em2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.285 — DNA-binding domain of intron-encoded endonucleases
Superfamily Superfamily superfamilyd.285.1 — DNA-binding domain of intron-encoded endonucleases
Family Family familyd.285.1.1 — DNA-binding domain of intron-encoded endonucleases

CATH v4.4 (2 domains)

Domain ID domain_id1u3eM01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology75 — Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1u3eM02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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7. Citations (1)