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5lfv

Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand

Method: X-RAY DIFFRACTION Dmax: 155.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Myelin-associated glycoprotein

Mus musculus

UniProt P20917

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 20–325 Not recorded ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol Resolution 2.30 Å R-free 0.254
2 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 20–325 Not recorded ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol Resolution 2.30 Å R-free 0.254

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 5LFV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LF5 Myelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with co-purified ligand Deposited 2016-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–508（489 aa）
Not recorded MAN alpha-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；100 mM NaCl, 20 mM Tris/HCl pH 7.0, 7.7 % PEG 4000 (w/v)
Resolution 3.80 Å R-free 0.228
5LFR Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 Deposited 2016-07-04 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–325（306 aa）
Not recorded MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol
Resolution 2.12 Å R-free 0.262
5LFR Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 Deposited 2016-07-04 Different ligand/ion Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 20–325（306 aa）
Not recorded MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.05 M tri-sodium citrate, 1.2 M ammonium sulfate, 3 % (w/v) isopropanol
Resolution 2.12 Å R-free 0.262
5LFU Myelin-associated glycoprotein (MAG) glycosylated and lysine-methylated full extracellular domain Deposited 2016-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–508（489 aa）
Not recorded MAN alpha-D-mannopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Crystals were grown from protein that was modified by reductive lysine methylation. Protein was concentrated to 8.4 mg/mL, which was mixed 1:1 with reservoir solution. Crystals grew in a condition containing 200 mM NaOAc and 20 % PEG3350 (w/v).
Resolution 4.30 Å R-free 0.295
6GZJ Complex between the dynein light chain DYNLL1/DLC8 and the specific domain of large myelin-associated glycoprotein L-MAG Deposited 2018-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 573–626（54 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate, and 25% (w/v) PEG 3350
Resolution 1.98 Å R-free 0.229

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

View Construct and Data Evidence
UniProt name MAG_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–308； UniProt 20–325 Author chain B； PDBConstruct 3–308； UniProt 20–325

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 5lfv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5lfv
Deposition date deposition_date2016-07-04
Structure title titleCrystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand
Keywords keywordsMyelin, Cell Adhesion, Signaling; 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_guinier36.09 Å
Radius of gyration Rg (electron density) rg_electron36.27 Å
Forward intensity I(0) i085924700.00
Molecular weight molecular_weight72178.0 kDa
Excluded volume excluded_volume89317 ų
Envelope volume envelope_volume122010 ų
Hydration-shell volume shell_volume30629 ų
Envelope diameter envelope_diameter161.3 Å
Shell Rg shell_rg38.32 Å
Envelope Rg envelope_rg37.33 Å
Shape Rg shape_rg36.25 Å
Total Rg total_rg36.48 Å
Total atoms total_atoms5061
Residues n_residues618
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 dmax155.5 Å
Rg (real space) rg_real36.66 Å
Rg uncertainty (real space) rg_real_error2.98 Å
I(0) (real space) i0_real8.5920e+07
I(0) uncertainty (real space) i0_real_error1.7950e+06
Rg (reciprocal space) rg_reciprocal36.30 Å
I(0) (reciprocal space) i0_reciprocal85900000.0000
Solution quality estimate total_estimate0.6995
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.3 Å
Skewness Skewness skewness0.711
Kurtosis Kurtosis kurtosis0.327
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7634000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.313; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.160; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)