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5llk

Crystal structure of human alpha-dystroglycan

Method: X-RAY DIFFRACTION Dmax: 79.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 52–315 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

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 5LLK 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 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
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
8UF4 Crystal structure of wildtype dystroglycan proteolytic domain (juxtamembrane domain) Deposited 2023-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 491–653（163 aa） Fragment：residues 491-653
Chain B 654–748（95 aa） Fragment：residues 654-748
Chain C 491–653（163 aa） Fragment：residues 491-653
Chain D 654–748（95 aa） Fragment：residues 654-748
Not recorded 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

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
Chains and sequence ranges Author chain A； PDBConstruct 3–266； UniProt 52–315

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 5llk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5llk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5llk
Deposition date deposition_date2016-07-27
Structure title titleCrystal structure of human alpha-dystroglycan
Keywords keywordsDystroglycan, Extraellular Matrix Adhesion, 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_guinier21.32 Å
Radius of gyration Rg (electron density) rg_electron20.58 Å
Forward intensity I(0) i010757800.00
Molecular weight molecular_weight24324.0 kDa
Excluded volume excluded_volume30486 ų
Envelope volume envelope_volume37416 ų
Hydration-shell volume shell_volume16501 ų
Envelope diameter envelope_diameter77.1 Å
Shell Rg shell_rg25.50 Å
Envelope Rg envelope_rg20.99 Å
Shape Rg shape_rg20.56 Å
Total Rg total_rg21.39 Å
Total atoms total_atoms3420
Residues n_residues226
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 dmax79.3 Å
Rg (real space) rg_real21.49 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real1.0760e+07
I(0) uncertainty (real space) i0_real_error1.4890e+05
Rg (reciprocal space) rg_reciprocal21.46 Å
I(0) (reciprocal space) i0_reciprocal10760000.0000
Solution quality estimate total_estimate0.7928
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.0 Å
Skewness Skewness skewness0.566
Kurtosis Kurtosis kurtosis-0.119
Angular range angular_range— – 0.3750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2323000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.553; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.645; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5llka1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.6 — Cadherin-like
Family Family familyb.1.6.0 — automated matches
Domain ID domain_idd5llka2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.272 — Dystroglycan, domain 2
Superfamily Superfamily superfamilyd.272.1 — Dystroglycan, domain 2
Family Family familyd.272.1.1 — Dystroglycan, domain 2

CATH v4.4 (2 domains)

Domain ID domain_id5llkA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5llkA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1040 — Dystroglycan, domain 2
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8. Citations (1)

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9. Files and Curves (10)