SAXSdb — 4bq7

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NEOGENIN

MUS MUSCULUS

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 883–1133	Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	RGM DOMAIN FAMILY MEMBER B × 1 （Q6NW40） RGM DOMAIN FAMILY MEMBER B × 1 （Q6NW40）	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 883–1133	Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	RGM DOMAIN FAMILY MEMBER B × 1 （Q6NW40） RGM DOMAIN FAMILY MEMBER B × 1 （Q6NW40）	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

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 4BQ7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BQ6 Crystal structure of the RGMB-NEO1 complex form 1 Deposited 2013-05-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	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	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	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
4BQ8 Crystal structure of the RGMB-NEO1 complex form 3 Deposited 2013-05-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 883–1083（201 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1083	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
4BQ9 Crystal structure of the FN5 and FN6 domains of NEO1, form 1 Deposited 2013-05-30	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 883–1083（201 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1083	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 2.91 Å R-free 0.230
4BQ9 Crystal structure of the FN5 and FN6 domains of NEO1, form 1 Deposited 2013-05-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 883–1083（201 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1083	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 2.91 Å R-free 0.230
4BQB Crystal structure of the FN5 and FN6 domains of NEO1, form 2 Deposited 2013-05-30	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 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223
4BQB Crystal structure of the FN5 and FN6 domains of NEO1, form 2 Deposited 2013-05-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223
4BQB Crystal structure of the FN5 and FN6 domains of NEO1, form 2 Deposited 2013-05-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223
4BQB Crystal structure of the FN5 and FN6 domains of NEO1, form 2 Deposited 2013-05-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.13 M POTASSIUM NITRATE, 13% PEG3350, pH 8.5	Resolution 2.70 Å R-free 0.223
4BQC Crystal structure of the FN5 and FN6 domains of NEO1 bound to SOS Deposited 2013-05-30	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 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.15 M POTASSIUM NITRATE, 15% PEG3350, pH 8.5	Resolution 3.20 Å R-free 0.259
4BQC Crystal structure of the FN5 and FN6 domains of NEO1 bound to SOS Deposited 2013-05-30	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 883–1133（251 aa） Fragment：FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.15 M POTASSIUM NITRATE, 15% PEG3350, pH 8.5	Resolution 3.20 Å R-free 0.259
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 765–964（200 aa） Fragment：FN4-5 (UNP residues 765-964) Chain D 765–964（200 aa） Fragment：FN4-5 (UNP residues 765-964)	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
4UI2 Crystal structure of the ternary RGMB-BMP2-NEO1 complex Deposited 2015-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 883–1133（251 aa） Fragment：5TH AND 6TH FN TYPE 3 LIKE DOMAINS	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
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain E 883–1123（241 aa） Chain F 883–1123（241 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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain K 883–1123（241 aa） Chain L 883–1123（241 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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain Q 883–1123（241 aa） Chain R 883–1123（241 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

8 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEO1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–254； UniProt 883–1133 Author chain B； PDBConstruct 4–254； UniProt 883–1133

RGM DOMAIN FAMILY MEMBER B

HOMO SAPIENS

UniProt Q6NW40

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 50–168 Chain F； UniProt 169–410	Fragment：RESIDUES 50-168 Fragment：RESIDUES 169-410	NEOGENIN × 1 （P97798）	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 50–168 Chain D； UniProt 169–410	Fragment：RESIDUES 50-168 Fragment：RESIDUES 169-410	NEOGENIN × 1 （P97798）	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

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 4BQ7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BQ6 Crystal structure of the RGMB-NEO1 complex form 1 Deposited 2013-05-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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
4BQ8 Crystal structure of the RGMB-NEO1 complex form 3 Deposited 2013-05-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different mutation/modification 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 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	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	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	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	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 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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: pentadecameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	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

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RGMB_HUMAN
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain C； PDBConstruct 4–122； UniProt 50–168 Author chain E； PDBConstruct 4–122； UniProt 50–168 Author chain D； PDBConstruct 1–242； UniProt 169–410 Author chain F； PDBConstruct 1–242； UniProt 169–410

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4bq7
Deposition date deposition_date	2013-05-30
Structure title title	Crystal structure of the RGMB-Neo1 complex form 2
Keywords keywords	CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.34 Å
Radius of gyration Rg (electron density) rg_electron	30.71 Å
Forward intensity I(0) i0	104045000.00
Molecular weight molecular_weight	81175.0 kDa
Excluded volume excluded_volume	101800 Å³
Envelope volume envelope_volume	131280 Å³
Hydration-shell volume shell_volume	36282 Å³
Envelope diameter envelope_diameter	103.9 Å
Shell Rg shell_rg	37.04 Å
Envelope Rg envelope_rg	30.70 Å
Shape Rg shape_rg	30.69 Å
Total Rg total_rg	31.36 Å
Total atoms total_atoms	5714
Residues n_residues	730
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.9 Å
Rg (real space) rg_real	31.29 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.0400e+08
I(0) uncertainty (real space) i0_real_error	1.5780e+06
Rg (reciprocal space) rg_reciprocal	31.31 Å
I(0) (reciprocal space) i0_reciprocal	104000000.0000
Solution quality estimate total_estimate	0.9042
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.6 Å
Skewness Skewness skewness	0.243
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13480000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.870

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NEOGENIN
Molecular weight formula_weight	29221.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5714

ETGTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTPKADSSDKMPNDQALGSAGKGSRLPDLGSDYKPPMSGSNSPHGSPTSPLDSNGTKHHHHHH

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	HOMO SAPIENS

Entity 2 Entity 2 polymer

Description description	RGM DOMAIN FAMILY MEMBER B
Molecular weight formula_weight	13318.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E

ETGQPAQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSSTNPEVTHDPCNYHSHAGAREHRRGDQNPPSYLFCGLFGD

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	HOMO SAPIENS

Entity 3 Entity 3 polymer

Description description	RGM DOMAIN FAMILY MEMBER B
Molecular weight formula_weight	27945.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

PHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHGCTDQKVYQAVTDDLPAAFVDGTTSGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDDGQGQVSAILGHSLPRTSLVQAWPGYTLETANTQCHEKMPVKDIYFQSCVFDLLTTGDANFTAAAHSALEDVEALHPRKERWHIFPSGTKHHHHHH

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	HOMO SAPIENS

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8. Citations (1)

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Unit-cell length a length_a	109.690 Å
Unit-cell length b length_b	109.690 Å
Unit-cell length c length_c	187.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 1 2
Space-group number int_tables_number	153
Crystal system crystal_system	—

Resolution resolution	6.601 Å
Low-resolution limit resolution_low	84.779 Å
R factor r_factor	0.2561
R_work r_work	0.2537
R_free r_free	0.2799

fit	/app/data/saxs_computation/bq/4bq7/4bq7.fit
pddf	/app/data/pr_computation/bq/4bq7/4bq7.pr.out
profile	/app/data/saxs_computation/bq/4bq7/4bq7.dat

Crystal structure of the RGMB-Neo1 complex form 2

1. Protein Identity and Related Structures Protein Identity & Related Structures

NEOGENIN

State in the Current Structure

Other States of the Same Protein in the Database

RGM DOMAIN FAMILY MEMBER B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)