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4plo

Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5)

Method: X-RAY DIFFRACTION Dmax: 132.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Netrin receptor DCC

OrganismNot specified

UniProt P70211

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 721–922 Fragment：FN4-4 (UNP residues 721-922) Netrin-1 × 2 （Q90922） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SO4 SULFATE ION × 10 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, 30% v/v Pentaerythritol ethoxylate Resolution 2.90 Å R-free 0.288

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 4PLO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3PZD Structure of the myosin X MyTH4-FERM/DCC complex Deposited 2010-12-14 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 1410–1445（36 aa） Fragment：P3 motif
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；8% PEG 8000, 10% glycerol, HEPES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 289K
Resolution 2.50 Å R-free 0.259

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

View Construct and Data Evidence
UniProt name DCC_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 3–204； UniProt 721–922

Netrin-1

Gallus gallus

UniProt Q90922

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 26–457 Fragment：LN-LE3 (UNP residues 26-457) Netrin receptor DCC × 2 （P70211） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SO4 SULFATE ION × 10 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, 30% v/v Pentaerythritol ethoxylate Resolution 2.90 Å R-free 0.288

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 4PLO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4PLM Crystal Structure of Chicken Netrin-1 (LN-LE3) Deposited 2014-05-18 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 26–457（432 aa） Fragment：LN-LE3 (UNP residues 26-457)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；NaoAc, NaCacodylate
Resolution 2.80 Å R-free 0.257
4PLM Crystal Structure of Chicken Netrin-1 (LN-LE3) Deposited 2014-05-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–457（432 aa） Fragment：LN-LE3 (UNP residues 26-457)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；NaoAc, NaCacodylate
Resolution 2.80 Å R-free 0.257
4PLN Crystal Structure of Chicken Netrin-1 (LN-LE3) complexed with mouse Neogenin (FN4-5) Deposited 2014-05-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 26–457（432 aa） Fragment：LN-LE3 (UNP residues 26-457)
Chain B 26–457（432 aa） Fragment：LN-LE3 (UNP residues 26-457)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Hepes pH 7.0, 12% PEG3350
Resolution 3.20 Å R-free 0.239
7LER Netrin-1 filament assembly Deposited 2021-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 48 PDB declaration: 48-meric
Chain A 26–458（433 aa）
Chain B 26–458（433 aa）
Chain C 26–458（433 aa）
Chain D 26–458（433 aa）
Chain E 26–458（433 aa）
Chain F 26–458（433 aa）
Chain G 26–458（433 aa）
Chain H 26–458（433 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 96 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；40% MPD, 100 mM Tris
Resolution 5.99 Å R-free 0.368
7LRF Netrin-1 in complex with SOS Deposited 2021-02-16 Different construct Different mutation/modification 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 26–458（433 aa）
Chain B 26–458（433 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293.15 K；20% PEG 8000, 100 mM CHES
Resolution 3.21 Å R-free 0.281
8TSM Crystal structure of chicken Netrin-1 LN LE1-2 Deposited 2023-08-11 Different construct 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 26–405（380 aa） Fragment：residues 26-405
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350
Resolution 3.90 Å R-free 0.319
9D77 Crystal form of Netrin-1 mimics nanotubes Deposited 2024-08-16 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 26–458（433 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；40% v/v 2-methyl-2,4-pentanediol; 5% w/v polyethylene glycol 8000; 100 mM 2-(N-morpholino)ethanesulfonic acid; pH 6.5
Resolution 3.40 Å R-free 0.335

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NET1_CHICK
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–432； UniProt 26–457

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 4plo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4plo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4plo
Deposition date deposition_date2014-05-18
Structure title titleCrystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5)
Keywords keywordselongated, complex, PROTEIN BINDING; PROTEIN BINDING
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_guinier36.08 Å
Radius of gyration Rg (electron density) rg_electron36.39 Å
Forward intensity I(0) i085814700.00
Molecular weight molecular_weight68700.0 kDa
Excluded volume excluded_volume83945 ų
Envelope volume envelope_volume117240 ų
Hydration-shell volume shell_volume31019 ų
Envelope diameter envelope_diameter139.6 Å
Shell Rg shell_rg36.38 Å
Envelope Rg envelope_rg36.98 Å
Shape Rg shape_rg36.32 Å
Total Rg total_rg36.60 Å
Total atoms total_atoms4796
Residues n_residues604
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 dmax132.1 Å
Rg (real space) rg_real36.51 Å
Rg uncertainty (real space) rg_real_error1.61 Å
I(0) (real space) i0_real8.5810e+07
I(0) uncertainty (real space) i0_real_error1.5280e+06
Rg (reciprocal space) rg_reciprocal36.24 Å
I(0) (reciprocal space) i0_reciprocal85790000.0000
Solution quality estimate total_estimate0.8128
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.0 Å
Skewness Skewness skewness0.565
Kurtosis Kurtosis kurtosis-0.205
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4309000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.552; Smooth: 0.930
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4ploA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id4ploB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4ploB02
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)