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7dta

Solution structure of the C-clamp domain from human HDBP1 in complex with DNA

Method: SOLUTION NMR Dmax: 42.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SLC2A4 regulator

Homo sapiens

UniProt Q9NR83

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 355–387 Not recorded ;DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3') ; × 1 ;DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3') ; × 1 ZN ZINC ION × 1 SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 10 mM sodium phosphate, 10 mM NaCl；Pressure 1 NMR sample composition：0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O | 95% H2O/5% 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 7DTA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9Z44 Isoreticular co-crystal 1 with symmetrical expanded duplex (31mer) containing insert sequence CCCGGCCGGA and loaded with C-clamp domain Deposited 2025-11-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain D 355–387（33 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；60mM magnesium acetate, 1.8M lithium sulfate, 50mM MES pH 6.5.The crystal was crosslinked with 50 mg/mL EDC overnight, and then looped into a solution of 50mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 90 micromolar C-clamp
Resolution 7.20 Å R-free 0.345

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S2A4R_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–33； UniProt 355–387

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 7dta

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7dta
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7dta
Deposition date deposition_date2021-01-04
Structure title titleSolution structure of the C-clamp domain from human HDBP1 in complex with DNA
Keywords keywordsC-clamp, zinc finger, unmethylated CpG binding, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.03 Å
Radius of gyration Rg (electron density) rg_electron12.98 Å
Forward intensity I(0) i01363730000.00
Molecular weight molecular_weight215740.0 kDa
Excluded volume excluded_volume229430 ų
Envelope volume envelope_volume19228 ų
Hydration-shell volume shell_volume11729 ų
Envelope diameter envelope_diameter46.4 Å
Shell Rg shell_rg19.59 Å
Envelope Rg envelope_rg14.36 Å
Shape Rg shape_rg12.93 Å
Total Rg total_rg13.17 Å
Total atoms total_atoms25060
Residues n_residues1100
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 dmax42.4 Å
Rg (real space) rg_real12.97 Å
Rg uncertainty (real space) rg_real_error0.21 Å
I(0) (real space) i0_real1.3640e+09
I(0) uncertainty (real space) i0_real_error1.2100e+07
Rg (reciprocal space) rg_reciprocal12.97 Å
I(0) (reciprocal space) i0_reciprocal1364000000.0000
Solution quality estimate total_estimate0.8939
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.0 Å
Skewness Skewness skewness0.164
Kurtosis Kurtosis kurtosis-0.429
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha241900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)