SAXSdb — 6z3m

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

Growth/differentiation factor 5

Homo sapiens

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 387–501 Chain B； UniProt 387–501	Not recorded	RGM domain family member B × 6 （Q6NW40） Neogenin × 2 （P97798） 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
2	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain G； UniProt 387–501 Chain H； UniProt 387–501	Not recorded	RGM domain family member B × 6 （Q6NW40） Neogenin × 2 （P97798） 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
3	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain M； UniProt 387–501 Chain N； UniProt 387–501	Not recorded	RGM domain family member B × 6 （Q6NW40） Neogenin × 2 （P97798） 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

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 6Z3M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WAQ Crystal structure of human Growth and Differentiation Factor 5 (GDF-5) Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 387–501（115 aa） Fragment：RESIDUES 387-501 (RESIDUES 6-120 OF MATURE GDF-5)	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions 25% 2-METHLY-2,4-PENTANEDIOL, 0.1M SODIUM CITRATE PH 4.0	Resolution 2.28 Å R-free 0.237
2BHK Crystal structure of human growth and differentiation factor 5 (GDF5) Deposited 2005-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 382–501（120 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；100 MM SODIUM ACETATE, PH 5.0 30% ISOPROPANOL 14 MG/ML PROTEIN HANGING DROP	Resolution 2.40 Å R-free 0.220
3EVS Crystal structure of the GDF-5:BMP receptor IB complex. Deposited 2008-10-13	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 B 387–501（115 aa） Fragment：UNP residues 387-501	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.25；294 K；0.1M sodium acetate, 50% PPG 400, 30mM magnesium sulfate, pH 5.25, VAPOR DIFFUSION, temperature 294K	Resolution 2.10 Å R-free 0.256
3QB4 Crystal structure of a TGF-beta ligand-receptor complex Deposited 2011-01-12	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 A 387–501（115 aa） Fragment：GDF-5, residues 387-501	Mutation：R57A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241
3QB4 Crystal structure of a TGF-beta ligand-receptor complex Deposited 2011-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 387–501（115 aa） Fragment：GDF-5, residues 387-501	Mutation：R57A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241
3QB4 Crystal structure of a TGF-beta ligand-receptor complex Deposited 2011-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 387–501（115 aa） Fragment：GDF-5, residues 387-501 Chain C 387–501（115 aa） Fragment：GDF-5, residues 387-501	Mutation：R57A Mutation：R57A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	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 382–501（120 aa） Chain C 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 382–501（120 aa） Chain C 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 382–501（120 aa） Chain D 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 382–501（120 aa） Chain D 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
6Z3G Repulsive Guidance Molecule A (RGMA) in complex with Growth Differentiation Factor 5 (GDF5) Deposited 2020-05-20	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 387–501（115 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.5, 24% v/v polyethylene glycol (PEG) 400.	Resolution 2.78 Å R-free 0.288
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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 387–501（115 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 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 387–501（115 aa） Chain B 387–501（115 aa）	Mutation：Y487K, Q489D Mutation：Y487K, Q489D	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
6Z3L Repulsive Guidance Molecule C (RGMC, Hemojuvelin, HJV, HFE2) in complex with Growth Differentiation Factor 5 (GDF5) Deposited 2020-05-20	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 387–501（115 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1 M LiCl, 0.1 M citric acid pH 4.0, 8% gamma-butyrolactone.	Resolution 2.51 Å R-free 0.267
7ZJF R399E, a mutated form of GDF5, for disease modification of osteoarthritis Deposited 2022-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.15；293 K；01 M Hepes, 32% PEG 400, 230 mM MgCl2, pH 8.15	Resolution 1.30 Å R-free 0.222
8BWL Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation factor 5 (GDF5) and calcium Deposited 2022-12-06	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 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；12.1% w/v PEG 1000, 12.1% w/v PEG 3350, 12.1% v/v MPD, 97 mM CaCl2, 0.097 M Bicine/Trizma pH 8.5	Resolution 1.96 Å R-free 0.212
8BWM Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation factor 5 (GDF5) and calcium, long-wavelength X-ray dataset (4042 eV) Deposited 2022-12-07	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 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；12.1% w/v PEG 1000, 12.1% w/v PEG 3350, 12.1% v/v MPD, 97 mM CaCl2, 0.097 M Bicine/Trizma pH 8.5	Resolution 2.50 Å R-free 0.278
8BWN Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation Factor 5 (GDF5) and calcium, long-wavelength X-ray dataset (4010 eV) Deposited 2022-12-07	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 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 100 mM CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5	Resolution 2.57 Å R-free 0.283
8E3G BMP2/GDF5 heterodimer Deposited 2022-08-17	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 382–501（120 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris, magnesium formate	Resolution 2.80 Å R-free 0.234
8E3G BMP2/GDF5 heterodimer Deposited 2022-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 382–501（120 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris, magnesium formate	Resolution 2.80 Å R-free 0.234

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GDF5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–117； UniProt 387–501 Author chain B； PDBConstruct 3–117； UniProt 387–501 Author chain G； PDBConstruct 3–117； UniProt 387–501 Author chain H； PDBConstruct 3–117； UniProt 387–501 Author chain M； PDBConstruct 3–117； UniProt 387–501 Author chain N； PDBConstruct 3–117； UniProt 387–501

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain C； UniProt 53–412 Chain D； UniProt 53–412 Chain S； UniProt 53–412 Chain T； UniProt 53–412 Chain c； UniProt 53–412 Chain d； UniProt 53–412	Not recorded	Growth/differentiation factor 5 × 2 （P43026） Neogenin × 2 （P97798） 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
2	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain I； UniProt 53–412 Chain J； UniProt 53–412 Chain U； UniProt 53–412 Chain V； UniProt 53–412 Chain i； UniProt 53–412 Chain j； UniProt 53–412	Not recorded	Growth/differentiation factor 5 × 2 （P43026） Neogenin × 2 （P97798） 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
3	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain O； UniProt 53–412 Chain P； UniProt 53–412 Chain W； UniProt 53–412 Chain X； UniProt 53–412 Chain o； UniProt 53–412 Chain p； UniProt 53–412	Not recorded	Growth/differentiation factor 5 × 2 （P43026） Neogenin × 2 （P97798） 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

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 6Z3M	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
4BQ7 Crystal structure of the RGMB-Neo1 complex form 2 Deposited 2013-05-30	Different construct Different mutation/modification Different oligomeric state 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：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	Different construct Different mutation/modification Different oligomeric state 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：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	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 mutation/modification 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 ligand/ion 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 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 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
7NDG Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B Deposited 2021-02-01	Different construct 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 mutation/modification 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 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RGMB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–363； UniProt 53–412 Author chain D； PDBConstruct 4–363； UniProt 53–412 Author chain I； PDBConstruct 4–363； UniProt 53–412 Author chain J； PDBConstruct 4–363； UniProt 53–412 Author chain O； PDBConstruct 4–363； UniProt 53–412 Author chain P； PDBConstruct 4–363； UniProt 53–412 Author chain S； PDBConstruct 4–363； UniProt 53–412 Author chain T； PDBConstruct 4–363； UniProt 53–412 Author chain U； PDBConstruct 4–363； UniProt 53–412 Author chain V； PDBConstruct 4–363； UniProt 53–412 Author chain W； PDBConstruct 4–363； UniProt 53–412 Author chain X； PDBConstruct 4–363； UniProt 53–412 Author chain c； PDBConstruct 4–363； UniProt 53–412 Author chain d； PDBConstruct 4–363； UniProt 53–412 Author chain i； PDBConstruct 4–363； UniProt 53–412 Author chain j； PDBConstruct 4–363； UniProt 53–412 Author chain o； PDBConstruct 4–363； UniProt 53–412 Author chain p； PDBConstruct 4–363； UniProt 53–412

Neogenin

Mus musculus

UniProt P97798

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain E； UniProt 883–1123 Chain F； UniProt 883–1123	Not recorded	Growth/differentiation factor 5 × 2 （P43026） RGM domain family member B × 6 （Q6NW40） 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
2	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain K； UniProt 883–1123 Chain L； UniProt 883–1123	Not recorded	Growth/differentiation factor 5 × 2 （P43026） RGM domain family member B × 6 （Q6NW40） 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
3	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain Q； UniProt 883–1123 Chain R； UniProt 883–1123	Not recorded	Growth/differentiation factor 5 × 2 （P43026） RGM domain family member B × 6 （Q6NW40） 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

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 6Z3M	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 mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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
4BQ7 Crystal structure of the RGMB-Neo1 complex form 2 Deposited 2013-05-30	Different construct Different mutation/modification Different oligomeric state 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	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	Different construct Different mutation/modification Different oligomeric state 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	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	Different construct Different mutation/modification Different oligomeric state 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 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 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 mutation/modification 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 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 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 mutation/modification 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

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEO1_MOUSE
Isoform	P97798-4
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 4–244； UniProt 883–1123 Author chain F； PDBConstruct 4–244； UniProt 883–1123 Author chain K； PDBConstruct 4–244； UniProt 883–1123 Author chain L； PDBConstruct 4–244； UniProt 883–1123 Author chain Q； PDBConstruct 4–244； UniProt 883–1123 Author chain R； PDBConstruct 4–244； UniProt 883–1123

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	6z3m
Deposition date deposition_date	2020-05-21
Structure title title	Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1).
Keywords keywords	;Repulsive Guidance Molecule, RGM, Bone Morphogenetic Protein, BMP, Growth Differentiation Factor 5, GDF5, Neogenin, axon guidance, TGFbeta signalling, brain development, iron metabolism, signaling protein ;; SIGNALING PROTEIN
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	87.65 Å
Radius of gyration Rg (electron density) rg_electron	88.38 Å
Forward intensity I(0) i0	1862880000.00
Molecular weight molecular_weight	359500.0 kDa
Excluded volume excluded_volume	447230 Å³
Envelope volume envelope_volume	920280 Å³
Hydration-shell volume shell_volume	94925 Å³
Envelope diameter envelope_diameter	309.5 Å
Shell Rg shell_rg	74.22 Å
Envelope Rg envelope_rg	82.94 Å
Shape Rg shape_rg	88.40 Å
Total Rg total_rg	88.09 Å
Total atoms total_atoms	25210
Residues n_residues	3257
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	230.1 Å
Rg (real space) rg_real	84.27 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.7930e+09
I(0) uncertainty (real space) i0_real_error	3.5740e+07
Rg (reciprocal space) rg_reciprocal	86.12 Å
I(0) (reciprocal space) i0_reciprocal	1854000000.0000
Solution quality estimate total_estimate	0.8919
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	115.0 Å
Skewness Skewness skewness	0.018
Kurtosis Kurtosis kurtosis	-0.759
Angular range angular_range	— – 0.0900 Å⁻¹
Current regularization parameter α current_alpha	1.1160
Highest regularization parameter α highest_alpha	42630000.0000
Real-space data points n_real_points	19
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 0.965; Sysdev: 1.000; Positv: 1.000; Valcen: 0.811; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Growth/differentiation factor 5
Molecular weight formula_weight	13405.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,G,H,M,N
Atom count atom_count	25210

MKRQGKRPSKNLKARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RGM domain family member B
Molecular weight formula_weight	41036.7 kDa
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,I,J,O,P,c,d,i,j,o,p,S,T,U,V,W,X

ETGQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSSTNPEVTHDPCNYHSHAGAREHRRGDQNPPSYLFCGLFGDPHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHGCTDQKVYQAVTDDLPAAFVDGTTSGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDDGQGQVSAILGHSLPRTSLVQAWPGYTLETANTQCHEKMPVKDIYFQSCVFDLLTTGDANFTAAAHSALEDVEALHPRKERWHIFPSSGTKHHHHHH

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	Neogenin
Molecular weight formula_weight	28031.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,K,L,Q,R

ETGTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTPKALGSAGKGSRLPDLGSDYKPPMSGSNSPHGSPTSPLDSNGTKHHHHHH

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 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	9

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8. Citations (1)

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Unit-cell length a length_a	279.480 Å
Unit-cell length b length_b	279.480 Å
Unit-cell length c length_c	142.370 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	108

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	5.501 Å
Low-resolution limit resolution_low	69.870 Å
R factor r_factor	0.3310
R_work r_work	0.3257
R_free r_free	0.4282

fit	/app/data/saxs_computation/z3/6z3m/6z3m.fit
pddf	/app/data/pr_computation/z3/6z3m/6z3m.pr.out
profile	/app/data/saxs_computation/z3/6z3m/6z3m.dat

Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1).

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

Growth/differentiation factor 5

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

Neogenin

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 (4)

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

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)