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7lrf

Netrin-1 in complex with SOS

Method: X-RAY DIFFRACTION Dmax: 196.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 Other combination Homooligomer Protein × 2 其他Polymer 10 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–458 Chain B； UniProt 26–458 Not recorded beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 7 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 2 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

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 7LRF 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 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 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 construct Different mutation/modification 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 oligomeric state 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
4PLO Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5) Deposited 2014-05-18 Different construct Different mutation/modification Different oligomeric state 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)
Not recorded 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
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
8TSM Crystal structure of chicken Netrin-1 LN LE1-2 Deposited 2023-08-11 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 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 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）
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 1
Chains and sequence ranges Author chain A； PDBConstruct 5–437； UniProt 26–458 Author chain B； PDBConstruct 5–437； UniProt 26–458

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 7lrf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7lrf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7lrf
Deposition date deposition_date2021-02-16
Structure title titleNetrin-1 in complex with SOS
Keywords keywordsself assembly, localization, sulfate binding, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier59.39 Å
Radius of gyration Rg (electron density) rg_electron62.03 Å
Forward intensity I(0) i0166246000.00
Molecular weight molecular_weight96239.0 kDa
Excluded volume excluded_volume115920 ų
Envelope volume envelope_volume209880 ų
Hydration-shell volume shell_volume32858 ų
Envelope diameter envelope_diameter213.6 Å
Shell Rg shell_rg50.13 Å
Envelope Rg envelope_rg60.55 Å
Shape Rg shape_rg62.26 Å
Total Rg total_rg60.95 Å
Total atoms total_atoms6722
Residues n_residues829
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 dmax196.2 Å
Rg (real space) rg_real60.78 Å
Rg uncertainty (real space) rg_real_error2.75 Å
I(0) (real space) i0_real1.6620e+08
I(0) uncertainty (real space) i0_real_error3.6790e+06
Rg (reciprocal space) rg_reciprocal58.16 Å
I(0) (reciprocal space) i0_reciprocal165500000.0000
Solution quality estimate total_estimate0.6004
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary30.2 Å
Skewness Skewness skewness0.532
Kurtosis Kurtosis kurtosis-0.732
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3433000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.216; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.152; Smooth: 0.001
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7lrfA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id7lrfB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
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8. Citations (1)

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9. Files and Curves (10)