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1d9n

SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1

Method: SOLUTION NMR Dmax: 34.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

METHYL-CPG-BINDING PROTEIN MBD1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–75 Fragment：METHYL-CPG-BINDING DOMAIN OF MBD1 No other associated polymer 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

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 1D9N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IG4 Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA Deposited 2001-04-17 Different construct Different oligomeric state Different experimental conditions 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 1
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 1d9n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d9n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d9n
Deposition date deposition_date1999-10-28
Structure title titleSOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF THE METHYLATION-DEPENDENT TRANSCRIPTIONAL REPRESSOR MBD1/PCM1
Keywords keywordsMBD, METHYL-CPG, PCM1, METHYLATION, DNA BINDING DOMAIN, GENE REGULATION; GENE REGULATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.14 Å
Radius of gyration Rg (electron density) rg_electron12.88 Å
Forward intensity I(0) i0654334000.00
Molecular weight molecular_weight212690.0 kDa
Excluded volume excluded_volume265020 ų
Envelope volume envelope_volume50492 ų
Hydration-shell volume shell_volume21876 ų
Envelope diameter envelope_diameter64.0 Å
Shell Rg shell_rg25.91 Å
Envelope Rg envelope_rg19.10 Å
Shape Rg shape_rg12.80 Å
Total Rg total_rg13.56 Å
Total atoms total_atoms29575
Residues n_residues1875
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 dmax34.8 Å
Rg (real space) rg_real12.51 Å
Rg uncertainty (real space) rg_real_error0.03 Å
I(0) (real space) i0_real6.2480e+08
I(0) uncertainty (real space) i0_real_error3.9920e+06
Rg (reciprocal space) rg_reciprocal13.16 Å
I(0) (reciprocal space) i0_reciprocal654300000.0000
Solution quality estimate total_estimate0.6812
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary15.0 Å
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.327
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.1490
Highest regularization parameter α highest_alpha8365000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.972; Stabil: 0.986; Sysdev: 0.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d9na_
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_id1d9nA00
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)