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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q6NW40 New Search
11PDB entries
15Biological assembly
43chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

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
4BQ6 Crystal structure of the RGMB-NEO1 complex form 1 Deposited 2013-05-30 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain E 50–168（119 aa） Fragment：ECTODOMAIN, RESIDUES 50-168
Chain F 169–410（242 aa） Fragment：ECTODOMAIN, RESIDUES 169-410
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5 0.2 M SODIUM ACETATE 30% PEG4000
Resolution 2.30 Å R-free 0.267
4BQ6 Crystal structure of the RGMB-NEO1 complex form 1 Deposited 2013-05-30 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 50–168（119 aa） Fragment：ECTODOMAIN, RESIDUES 50-168
Chain D 169–410（242 aa） Fragment：ECTODOMAIN, RESIDUES 169-410
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5 0.2 M SODIUM ACETATE 30% PEG4000
Resolution 2.30 Å R-free 0.267
4BQ7 Crystal structure of the RGMB-Neo1 complex form 2 Deposited 2013-05-30 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain E 50–168（119 aa） Fragment：RESIDUES 50-168
Chain F 169–410（242 aa） Fragment：RESIDUES 169-410
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5, 0.2 M LITHIUM SULPHATE, 25 % PEG3350
Resolution 6.60 Å R-free 0.280
4BQ7 Crystal structure of the RGMB-Neo1 complex form 2 Deposited 2013-05-30 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 50–168（119 aa） Fragment：RESIDUES 50-168
Chain D 169–410（242 aa） Fragment：RESIDUES 169-410
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL, PH 8.5, 0.2 M LITHIUM SULPHATE, 25 % PEG3350
Resolution 6.60 Å R-free 0.280
4BQ8 Crystal structure of the RGMB-NEO1 complex form 3 Deposited 2013-05-30 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 50–168（119 aa） Fragment：ECTODOMAIN, RESIDUES 50-168
Chain C 169–410（242 aa） Fragment：ECTODOMAIN, RESIDUES 169-410
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；0.1 M SODIUM ACETATE, PH 4.6, 0.18 M POTASSIUM ACETATE, 18 % PEG 3350
Resolution 2.80 Å R-free 0.199
4UHZ Crystal structure of the human RGMB-BMP2 complex, crystal form 1 Deposited 2015-03-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 52–137（86 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 52-137
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions 2 M AMMONIUM SULPHATE, 8% (V/V) 2,5- HEXANEDIOL
Resolution 2.85 Å R-free 0.229
4UI0 Crystal structure of the human RGMB-BMP2 complex, crystal form 2 Deposited 2015-03-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 53–136（84 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 53-136
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 FLC CITRATE ANION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；0.08 M CITRIC ACID PH 4.0, 15% (V/V) MPD
Resolution 2.80 Å R-free 0.267
4UI2 Crystal structure of the ternary RGMB-BMP2-NEO1 complex Deposited 2015-03-27 Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count
Chain C 50–168（119 aa） Fragment：RESIDUES 50-168
Chain D 169–410（242 aa） Fragment：RESIDUES 169-240
Not recorded SRT S,R MESO-TARTARIC ACID × 6 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 1.5 M AMMONIUM SULPHATE, 12% (V/V) GLYCEROL
Resolution 3.15 Å R-free 0.236
6Z3H Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 2) Deposited 2020-05-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain B 53–136（84 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M (NH4)2SO4, 0.1 M sodium acetate pH 4.6, 35% w/v pentaerythritol ethoxylate (15/4 EO/OH; average MW 797 Da)
Resolution 3.16 Å R-free 0.268
6Z3J Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 1) Deposited 2020-05-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 53–136（84 aa）
Chain D 53–136（84 aa）
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；294 K；0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 25% v/v PEG 3350.
Resolution 1.65 Å R-free 0.219
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain C 53–412（360 aa）
Chain D 53–412（360 aa）
Chain S 53–412（360 aa）
Chain T 53–412（360 aa）
Chain c 53–412（360 aa）
Chain d 53–412（360 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000
Resolution 5.50 Å R-free 0.428
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21 Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain I 53–412（360 aa）
Chain J 53–412（360 aa）
Chain U 53–412（360 aa）
Chain V 53–412（360 aa）
Chain i 53–412（360 aa）
Chain j 53–412（360 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000
Resolution 5.50 Å R-free 0.428
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21 Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain O 53–412（360 aa）
Chain P 53–412（360 aa）
Chain W 53–412（360 aa）
Chain X 53–412（360 aa）
Chain o 53–412（360 aa）
Chain p 53–412（360 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000
Resolution 5.50 Å R-free 0.428
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 C 169–412（244 aa）
Chain F 169–412（244 aa）
Chain I 169–412（244 aa）
Chain M 53–168（116 aa）
Chain N 53–168（116 aa）
Chain O 53–168（116 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 C 135–168（34 aa）
Chain D 169–323（155 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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.