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1ig4

Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA

Method: SOLUTION NMR Dmax: 58.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methyl-CpG Binding Protein

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 1–75 Fragment：Methyl-CpG-binding domain 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3' × 2 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

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 1IG4 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 experimental conditions 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
4D4W Solution structure of human MBD1 CXXC1 domain Deposited 2014-10-31 Different construct Different oligomeric state Different experimental conditions 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
5W9Q Zinc finger region of MBD1 in complex with CpG DNA Deposited 2017-06-23 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 330–388（59 aa） Fragment：Zinc finger region (UNP residues 330-388)
Not recorded 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
5W9Q Zinc finger region of MBD1 in complex with CpG DNA Deposited 2017-06-23 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 330–388（59 aa） Fragment：Zinc finger region (UNP residues 330-388)
Not recorded 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
6D1T Complex of MBD1-MBD and methylated DNA Deposited 2018-04-12 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 1–77（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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MBD1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–75； UniProt 1–75

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

SAXS profile for 1ig4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ig4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ig4
Deposition date deposition_date2001-04-17
Structure title titleSolution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA
Keywords keywordsPROTEIN-DNA COMPLEX, ALPHA-BETA, DOUBLE HELIX, RECOGNITION VIA BETA-SHEET, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.34 Å
Radius of gyration Rg (electron density) rg_electron15.40 Å
Forward intensity I(0) i02394620000.00
Molecular weight molecular_weight316940.0 kDa
Excluded volume excluded_volume355260 ų
Envelope volume envelope_volume36929 ų
Hydration-shell volume shell_volume17245 ų
Envelope diameter envelope_diameter67.3 Å
Shell Rg shell_rg24.36 Å
Envelope Rg envelope_rg19.06 Å
Shape Rg shape_rg15.31 Å
Total Rg total_rg15.70 Å
Total atoms total_atoms38980
Residues n_residues1940
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.3 Å
Rg (real space) rg_real15.30 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real2.3950e+09
I(0) uncertainty (real space) i0_real_error3.1050e+07
Rg (reciprocal space) rg_reciprocal15.30 Å
I(0) (reciprocal space) i0_reciprocal2395000000.0000
Solution quality estimate total_estimate0.7297
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.106
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha451800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.539; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.865; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ig4a_
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.10.1.3 — Methyl-CpG-binding domain, MBD

CATH v4.4 (1 domains)

Domain ID domain_id1ig4A00
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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8. Citations (3)

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9. Files and Curves (10)