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8uf4

Crystal structure of wildtype dystroglycan proteolytic domain (juxtamembrane domain)

Method: X-RAY DIFFRACTION Dmax: 83.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

a-dystroglycan

Homo sapiens

UniProt Q14118

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 491–653 Chain B； UniProt 654–748 Chain C； UniProt 491–653 Chain D； UniProt 654–748 Fragment：residues 491-653 Fragment：residues 654-748 CA CALCIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；295 K；0.1 M Tris, 0.2 M lithium sulfate, 20% PEG 4000 Resolution 2.43 Å R-free 0.275

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 8UF4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EG4 STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE Deposited 2000-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 881–895（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；ammonium sulfate, glycerol, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.249
2MK7 Tetra-O-GalNAc glycosylated mucin sequence from alpha dystroglycan mucin domain Deposited 2014-02-02 Different construct Different mutation/modification 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 419–427（9 aa） Fragment：mucin domain peptide (UNP residues 419-427)
Non-standard monomer：Yes (specific site not provided by mmCIF) A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 4 SOLUTION NMR
NMR measurement conditions pH 4.5；288 K；Pressure ambient
NMR sample composition 2-10 mM aDG mucin domain peptide, 100% D2O | 100% D2O
NMR sample composition 2-10 mM aDG mucin domain peptide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5GGP Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 316–325（10 aa）
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；MES-NaOH, LiCl2, Na acetate, PEG-6000
Resolution 1.60 Å R-free 0.246
5GGP Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 316–325（10 aa）
Not recorded NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；MES-NaOH, LiCl2, Na acetate, PEG-6000
Resolution 1.60 Å R-free 0.246
5LLK Crystal structure of human alpha-dystroglycan Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 52–315（264 aa） Fragment：UNP residues 52-315
Mutation：R168H EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；0.8 M Sodium Citrate
Resolution 1.80 Å R-free 0.195
6JJY Crystal Structure of KIBRA and beta-Dystroglycan Deposited 2019-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain U 877–895（19 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；3.0-4.0M NaCl, 100mM Bis-Tris (pH 6.5)
Resolution 2.30 Å R-free 0.253

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DAG1_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–163； UniProt 491–653 Author chain C； PDBConstruct 1–163； UniProt 491–653 Author chain B； PDBConstruct 1–95； UniProt 654–748 Author chain D； PDBConstruct 1–95； UniProt 654–748

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 8uf4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8uf4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8uf4
Deposition date deposition_date2023-10-03
Structure title titleCrystal structure of wildtype dystroglycan proteolytic domain (juxtamembrane domain)
Keywords keywordsSEA domain, mechanoreceptor, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.83 Å
Radius of gyration Rg (electron density) rg_electron23.77 Å
Forward intensity I(0) i043627900.00
Molecular weight molecular_weight50986.0 kDa
Excluded volume excluded_volume63746 ų
Envelope volume envelope_volume78066 ų
Hydration-shell volume shell_volume27479 ų
Envelope diameter envelope_diameter86.2 Å
Shell Rg shell_rg30.77 Å
Envelope Rg envelope_rg23.83 Å
Shape Rg shape_rg23.75 Å
Total Rg total_rg24.63 Å
Total atoms total_atoms3595
Residues n_residues454
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 dmax83.2 Å
Rg (real space) rg_real24.75 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real4.3630e+07
I(0) uncertainty (real space) i0_real_error6.5670e+05
Rg (reciprocal space) rg_reciprocal24.77 Å
I(0) (reciprocal space) i0_reciprocal43630000.0000
Solution quality estimate total_estimate0.8812
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1 Å
Skewness Skewness skewness0.268
Kurtosis Kurtosis kurtosis-0.340
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7677000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.947
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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 (10)