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5w9q

Zinc finger region of MBD1 in complex with CpG DNA

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

Methyl-CpG-binding domain protein 1

Homo sapiens

UniProt Q9UIS9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 330–388 Fragment：Zinc finger region (UNP residues 330-388) dna × 2 ZN ZINC ION × 2 UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；291 K；25% PEG-400, 0.2 M magnesium chloride, 0.1 M hepes Resolution 1.80 Å R-free 0.253
2 Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain B； UniProt 330–388 Fragment：Zinc finger region (UNP residues 330-388) dna × 2 ZN ZINC ION × 2 UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；291 K；25% PEG-400, 0.2 M magnesium chloride, 0.1 M hepes Resolution 1.80 Å R-free 0.253

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5W9Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D9N SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1 Deposited 1999-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–75（75 aa） Fragment：METHYL-CPG-BINDING DOMAIN OF MBD1
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 50mM KCL；Pressure 1
NMR sample composition 1.3MM MBD U-15N,13C; 20MM PHOSPHATE BUFFER; 50MM KCL; 5MM DTT
Resolution not provided
1IG4 Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA Deposited 2001-04-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–75（75 aa） Fragment：Methyl-CpG-binding domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K
NMR sample composition 1.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer | 90% H2O/10% D2O
NMR sample composition 1.3mM MBD1(U-15N,13C)-DNA Complex; 20mM phosphate buffer | 100% D2O
NMR sample composition 1mM MBD1(U-15N)-DNA Complex; 20mM phosphate buffer | 90% H2O/10% D2O
Resolution not provided
4D4W Solution structure of human MBD1 CXXC1 domain Deposited 2014-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 167–222（56 aa） Fragment：RESIDUES 167-222
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 0.25；Pressure 1.0
NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 0.25；Pressure 1.0
NMR sample composition 95% H2O/5% D2O
Resolution not provided
6D1T Complex of MBD1-MBD and methylated DNA Deposited 2018-04-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–77（77 aa） Fragment：residues 1-77
Not recorded UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；30% PEG-550-MME, 0.1 M magnesium chloride, 0.1 M HEPES
Resolution 2.25 Å R-free 0.269

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MBD1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–60； UniProt 330–388 Author chain B； PDBConstruct 2–60； UniProt 330–388

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.

SAXS scattering curve SAXS Profile

暂无 SAXS 图

P(r) Distance Distribution P(r) Distribution

暂无 P(r) 图
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5w9q
Deposition date deposition_date2017-06-23
Structure title titleZinc finger region of MBD1 in complex with CpG DNA
Keywords keywordszinc finger, dna-binding, CXXC3, Structural Genomics, Structural Genomics Consortium, SGC, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (0)