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3vyq

Crystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1

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

Methyl-CpG-binding domain protein 4

Mus musculus

UniProt Q9Z2D7

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(*AP*CP*AP*TP*CP*(5CM)P*GP*GP*TP*GP*A)-3') ; × 1 ;DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*AP*TP*GP*T)-3') ; × 1 ZINC ION × 3 1,2-ETHANEDIOL × 1 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1ngn

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3vxv 3vxx 3vyb 3vyq 4evv 4ew0 4ew4

7 assemblies

View Construct and Data Evidence
UniProt name MBD4_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–74； UniProt 63–136 Author chain D； PDBConstruct 1–74； UniProt 63–136

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_id3vyq
Deposition date deposition_date2012-10-02
Structure title titleCrystal structure of the methyl CpG Binding Domain of MBD4 in complex with the 5mCG/TG sequence in space group P1
Keywords keywordsmethyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex; HYDROLASE/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.

3vyq__assembly_1__model_1

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

Download this curve (.dat)

3vyq__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.

3vyq__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）19.58 Å
Rg (electron density)19.88 Å
Total Rg20.72 Å
Atom count1466
Residues146
Excluded volume25036 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3vyq__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 (6)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3vyqa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.10 — DNA-binding domain
Superfamily Superfamily superfamilyd.10.1 — DNA-binding domain
Family Family familyd.10.1.0 — automated matches
Domain ID domain_idd3vyqd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.10 — DNA-binding domain
Superfamily Superfamily superfamilyd.10.1 — DNA-binding domain
Family Family familyd.10.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3vyqA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology890 — Methyl-cpg-binding Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Methyl-cpg-binding Protein 2; Chain A
Domain ID domain_id3vyqD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology890 — Methyl-cpg-binding Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Methyl-cpg-binding Protein 2; Chain A
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7. Citations (1)