SAXSdb — 4ui0

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

BONE MORPHOGENETIC PROTEIN 2

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 283–396 Chain B； UniProt 283–396	Fragment：C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396	RGM DOMAIN FAMILY MEMBER B × 1 （Q6NW40） 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

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 4UI0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ES7 COMPLEX BETWEEN BMP-2 AND TWO BMP RECEPTOR IA ECTODOMAINS Deposited 2000-04-07	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 283–396（114 aa） Chain C 283–396（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；sodium acetate, imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.90 Å R-free 0.229
1REU Structure of the bone morphogenetic protein 2 mutant L51P Deposited 2003-11-07	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 294–396（103 aa） Fragment：mature part	Mutation：L51P	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；lithium sulfate, tert-butanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.235
1REU Structure of the bone morphogenetic protein 2 mutant L51P Deposited 2003-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 294–396（103 aa） Fragment：mature part	Mutation：L51P	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；lithium sulfate, tert-butanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.235
1REW Structural refinement of the complex of bone morphogenetic protein 2 and its type IA receptor Deposited 2003-11-07	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 283–396（114 aa） Fragment：mature part Chain B 283–396（114 aa） Fragment：mature part	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；280 K；sodium acetate, imidazole, glucose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K	Resolution 1.86 Å R-free 0.229
2GOO Ternary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD Deposited 2006-04-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 283–396（114 aa） Fragment：Residues 283-396 Chain D 283–396（114 aa） Fragment：Residues 283-396	Not recorded	NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；4M sodium formate, 100mM Hepes, 3% dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.259
2H62 Crystal structure of a ternary ligand-receptor complex of BMP-2 Deposited 2006-05-30	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 283–396（114 aa） Chain B 283–396（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；294 K；50% PPG400, 0.1M Bis-Tris, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.85 Å R-free 0.225
2H64 Crystal structure of a ternary ligand-receptor complex of BMP-2 Deposited 2006-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 283–396（114 aa）	Mutation：L100K, N102D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.75；294 K；30% PEG3350, 0.1M Tris-HCl pH 8.75, 0.2M NH4CH3COO, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.92 Å R-free 0.264
2QJ9 Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B1 Deposited 2007-07-06	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 283–396（114 aa） Fragment：mature part (residues 283-396) Chain B 283–396（114 aa） Fragment：mature part (residues 283-396)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.44 Å R-free 0.253
2QJA Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B12 Deposited 2007-07-06	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 283–396（114 aa） Fragment：mature part (residues 283-396) Chain B 283–396（114 aa） Fragment：mature part (residues 283-396)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.254
2QJB Crystal structure analysis of BMP-2 in complex with BMPR-IA variant IA/IB Deposited 2007-07-06	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 283–396（114 aa） Fragment：mature part (residues 283-396) Chain B 283–396（114 aa） Fragment：mature part (residues 283-396)	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.263
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05	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 283–396（114 aa） Chain B 283–396（114 aa）	Mutation：F41M, Y91M Mutation：F41M, Y91M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.245
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05	Different construct Different mutation/modification 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 283–396（114 aa） Chain B 283–396（114 aa）	Mutation：F41M, Y91M Mutation：F41M, Y91M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.245
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 283–396（114 aa）	Mutation：F41M, Y91M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.245
3BK3 Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2 Deposited 2007-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 283–396（114 aa）	Mutation：F41M, Y91M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；2.2M ammonium phosphate, 0.1M Tris pH 7.5, 8% glycerol, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.245
3BMP HUMAN BONE MORPHOGENETIC PROTEIN-2 (BMP-2) Deposited 1999-03-12	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 283–396（114 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 100 MM LITHIUM SULFATE, 12% TERT-BUTANOL, 50 MM CITRATE, PH 5.4	Resolution 2.70 Å R-free 0.278
4N1D Nodal/BMP2 chimera NB250 Deposited 2013-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 283–305（23 aa） Chain A 362–396（35 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；0.2M NaCl, 0.1 M Na acetate pH 4.6, 30% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.91 Å R-free 0.204
4UHY Crystal structure of the human RGMA-BMP2 complex Deposited 2015-03-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 283–396（114 aa） Fragment：C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396 Chain B 283–396（114 aa） Fragment：C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；0.1 M CITRIC ACID, PH 4.0, 20% (V/V) 2-METHYL-2,4-PENTANEDIOL (MPD), 0.2 M GLYCINE	Resolution 3.20 Å R-free 0.264
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 A 283–396（114 aa） Fragment：C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396	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
4UI1 Crystal structure of the human RGMC-BMP2 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 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 283–396（114 aa） Fragment：C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396	Not recorded	NO3 NITRATE ION × 2 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% (W/V) PEG3350, 0.2 M AMMONIUM NITRATE, PH 7.5	Resolution 2.35 Å R-free 0.238
4UI1 Crystal structure of the human RGMC-BMP2 complex Deposited 2015-03-27	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 B 283–396（114 aa） Fragment：C-TERMINAL DOMAIN SIGNALING DOMAIN, RESIDUES 283-396	Not recorded	NO3 NITRATE ION × 4 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% (W/V) PEG3350, 0.2 M AMMONIUM NITRATE, PH 7.5	Resolution 2.35 Å R-free 0.238
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 B 283–396（114 aa） Fragment：C-TERMINAL DOMAIN SIGNALING DOMAIN	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
6OMN Glycosylated BMP2 homodimer Deposited 2019-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 289–396（108 aa） Chain F 289–396（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100mM TrisHCl pH 8.5, 100mM NaCl, 12% MPD	Resolution 2.68 Å R-free 0.243
6OMN Glycosylated BMP2 homodimer Deposited 2019-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 289–396（108 aa） Chain H 289–396（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100mM TrisHCl pH 8.5, 100mM NaCl, 12% MPD	Resolution 2.68 Å R-free 0.243
7AG0 Complex between the bone morphogenetic protein 2 and its antagonist Noggin Deposited 2020-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 283–396（114 aa）	Not recorded	GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；1.4 M NaKPO4	Resolution 3.10 Å R-free 0.280
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 A 283–396（114 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 C 283–396（114 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

19 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BMP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–114； UniProt 283–396 Author chain B； PDBConstruct 1–114； UniProt 283–396

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 C； UniProt 53–136	Fragment：N-TERMINAL DOMAIN, RESIDUES 53-136	BONE MORPHOGENETIC PROTEIN 2 × 2 （P12643） 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

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 4UI0	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 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 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 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 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 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 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
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 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
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 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 14 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 4–87； UniProt 53–136

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	4ui0
Deposition date deposition_date	2015-03-27
Structure title title	Crystal structure of the human RGMB-BMP2 complex, crystal form 2
Keywords keywords	;SIGNALING PROTEIN, REPULSIVE GUIDANCE MOLECULE, BONE MORPHOGENETIC PROTEIN PATHWAY, HEMOJUVELIN, MORPHOGEN, AXON GUIDANCE, CELL SURFACE RECEPTOR SIGNALING ;; 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	21.95 Å
Radius of gyration Rg (electron density) rg_electron	21.70 Å
Forward intensity I(0) i0	16229500.00
Molecular weight molecular_weight	29262.0 kDa
Excluded volume excluded_volume	36149 Å³
Envelope volume envelope_volume	45382 Å³
Hydration-shell volume shell_volume	18452 Å³
Envelope diameter envelope_diameter	81.5 Å
Shell Rg shell_rg	27.23 Å
Envelope Rg envelope_rg	22.24 Å
Shape Rg shape_rg	21.75 Å
Total Rg total_rg	22.34 Å
Total atoms total_atoms	2040
Residues n_residues	261
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	79.6 Å
Rg (real space) rg_real	22.13 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.6230e+07
I(0) uncertainty (real space) i0_real_error	2.0510e+05
Rg (reciprocal space) rg_reciprocal	22.10 Å
I(0) (reciprocal space) i0_reciprocal	16230000.0000
Solution quality estimate total_estimate	0.6225
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.579
Kurtosis Kurtosis kurtosis	0.030
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3296000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.702; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	BONE MORPHOGENETIC PROTEIN 2
Molecular weight formula_weight	12923.9 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	2060

QAKHKQRKRLKSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR

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	10532.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ETGQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSSTNPEVTHGTKHHHHHH

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 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4ui0a_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.2 — Transforming growth factor (TGF)-beta

Domain ID domain_id	d4ui0b_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (2 domains)

Domain ID domain_id	4ui0A00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	4ui0B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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8. Citations (1)

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Unit-cell length a length_a	85.021 Å
Unit-cell length b length_b	85.021 Å
Unit-cell length c length_c	115.182 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 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2344
R_work r_work	0.2327
R_free r_free	0.2665

fit	/app/data/saxs_computation/ui/4ui0/4ui0.fit
pddf	/app/data/pr_computation/ui/4ui0/4ui0.pr.out
profile	/app/data/saxs_computation/ui/4ui0/4ui0.dat

Crystal structure of the human RGMB-BMP2 complex, crystal form 2

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

BONE MORPHOGENETIC PROTEIN 2

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)