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6f57

Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA

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

DNA (cytosine-5)-methyltransferase 3A

Homo sapiens

UniProt Q9Y6K1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 DNA (cytosine-5)-methyltransferase 3-like × 1 （Q9UJW3） ;DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3') ; × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with all polymers
2 Protein–DNA Heteromer Protein 2 DNA 2 DNA (cytosine-5)-methyltransferase 3-like × 1 （Q9UJW3） ;DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3') ; × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
3a1a 3llr 3llr 3llr 3llr 3llr 8ba5

7 assemblies

Homodimer

None

Homotetramer
8tdr 8tdr 8te1 8te1 8te3 8te3 8te4 8te4

8 assemblies

Other homooligomers
9mpo

1 assemblies

Heteromeric or nucleic-acid complex
2qrv 2qrv 3a1b 3svm 3svm 4qbq 4qbr 4qbr 4qbs 4u7p 4u7t 5yx2

41 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DNM3A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–285； UniProt 628–912 Author chain D； PDBConstruct 1–285； UniProt 628–912

DNA (cytosine-5)-methyltransferase 3-like

Homo sapiens

UniProt Q9UJW3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 DNA (cytosine-5)-methyltransferase 3A × 1 （Q9Y6K1） ;DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3') ; × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with all polymers
2 Protein–DNA Heteromer Protein 2 DNA 2 DNA (cytosine-5)-methyltransferase 3A × 1 （Q9Y6K1） ;DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3') ; × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2pv0 2pv0 2pv0

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2pvc 2pvc 2pvc 2qrv 2qrv 4u7p 4u7t 5yx2 6brr 6f57 6f57 6kda

36 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DNM3L_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–209； UniProt 178–386 Author chain C； PDBConstruct 1–209； UniProt 178–386

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_id6f57
Deposition date deposition_date2017-12-01
Structure title titleCrystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA
Keywords keywordsDNMT3A, DNMT3L, DNA methylation, DNA binding protein, transferase-DNA complex; transferase/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.

6f57__assembly_1__model_1

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

Download this curve (.dat)

6f57__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.

6f57__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）25.40 Å
Rg (electron density)24.71 Å
Total Rg25.42 Å
Atom count3794
Residues454
Excluded volume66074 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6f57__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6f57__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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6f57B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id6f57C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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7. Citations (1)