Current Protein Identity：O95631
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4URT The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC Deposited 2014-07-02 | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
39–453（415 aa）
Fragment：VI AND V DOMAINS, RESIDUES 39-453
|
Not recorded | CA CALCIUM ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 18 GOL GLYCEROL × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 6；0.1M MES PH 6.0, 0.15M AMMONIUM SULFATE AND 15% (W/V) PEG 4000
|
Resolution 3.10 Å R-free 0.265 |
| 6FKQ THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A FRAGMENT OF DRAXIN Deposited 2018-01-24 | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
39–453（415 aa）
|
Not recorded | CA CALCIUM ION × 1 SO4 SULFATE ION × 10 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；298 K；1.6 M AMMONIUM SULPHATE AND 0.1 M
SODIUM CITRATE, AT PH 4 TO PH 5, VAPOR DIFFUSION, TEMPERATURE
298K
|
Resolution 3.07 Å R-free 0.271 |
| 7NDG Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B Deposited 2021-02-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: pentadecameric（15） Review required |
Chain A
25–453（429 aa）
Chain D
25–453（429 aa）
Chain G
25–453（429 aa）
|
Not recorded | CA CALCIUM ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；10 mM HEPES pH 7.5, 150 mM NaCl, 2 mM CaCl2, 1 mM sucrose octasulfate, 0.01% NaN3
cryo-EM vitrification conditions
Cryogen ETHANE；Lacey carbon grids with 3 nm ultrathin carbon support film were glow discharged for 30 seconds at high RF level using Harrick Plasma Cleaner, model PDC-002-CE, and then 3.5 microl of the sample was pipetted per grid. Excess protein was blotted away for 3 seconds using filter paper (round filter paper for Vitrobot from Agar Scientific, catalogue number 47000-100) and Vitrobot Mark IV (Thermo Fisher Scientific) (relative force -15) at 95-100% humidity. Grids were plunge frozen in liquid ethane.
|
Resolution 5.98 Å |
| 7NE0 Structure of the ternary complex between Netrin-1, Repulsive-Guidance Molecule-B (RGMB) and Neogenin Deposited 2021-02-02 | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
24–453（430 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；298.15 K；0.1 M imidazole/MES pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 30 mM sodium nitrate, 30 mM sodium phosphate, 30 mM ammonium sulphate
|
Resolution 3.25 Å R-free 0.263 |
| 7NE1 Structure of the complex between Netrin-1 and its receptor Neogenin Deposited 2021-02-02 | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
24–453（430 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 NO3 NITRATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.2 M ammonium nitrate, 20% w/v PEG 3350, 40 mM potassium/sodium tartrate
|
Resolution 3.15 Å R-free 0.239 |