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5lf5

Myelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with co-purified ligand

Method: X-RAY DIFFRACTION Dmax: 184.7 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 Homooligomer Protein × 2 其他Polymer 4 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 20–508 Not recorded alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose × 2 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

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 5LF5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LFR Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 Deposited 2016-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 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
5LFV Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand Deposited 2016-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 × 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
5LFV Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand Deposited 2016-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 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
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 6 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 3–491； UniProt 20–508

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 5lf5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lf5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5lf5
Deposition date deposition_date2016-06-30
Structure title titleMyelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with co-purified 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_guinier55.61 Å
Radius of gyration Rg (electron density) rg_electron57.71 Å
Forward intensity I(0) i046534000.00
Molecular weight molecular_weight55264.0 kDa
Excluded volume excluded_volume69054 ų
Envelope volume envelope_volume119980 ų
Hydration-shell volume shell_volume22291 ų
Envelope diameter envelope_diameter195.7 Å
Shell Rg shell_rg40.91 Å
Envelope Rg envelope_rg58.35 Å
Shape Rg shape_rg57.73 Å
Total Rg total_rg56.84 Å
Total atoms total_atoms3887
Residues n_residues484
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 dmax184.7 Å
Rg (real space) rg_real56.94 Å
Rg uncertainty (real space) rg_real_error2.18 Å
I(0) (real space) i0_real4.6530e+07
I(0) uncertainty (real space) i0_real_error9.5060e+05
Rg (reciprocal space) rg_reciprocal54.45 Å
I(0) (reciprocal space) i0_reciprocal46360000.0000
Solution quality estimate total_estimate0.5586
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4 Å
Skewness Skewness skewness0.564
Kurtosis Kurtosis kurtosis-0.713
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1309000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.077; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.026; Smooth: 0.001
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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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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5lf5A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5lf5A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5lf5A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5lf5A04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)