SAXSdb — 9dpy

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

Bone morphogenetic protein 10

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 320–424 Chain B； UniProt 320–424	Mutation：N357F, Y358F, A374T, Y409L, F411Y	PO4 PHOSPHATE ION × 13 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；25% (v/v) 1,2-propanediol, 100 mM sodium phosphate dibasic/potassium phosphate monobasic pH 6.2, 10% (v/v) glycerol	Resolution 1.77 Å R-free 0.251

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 9DPY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6SF1 Bone morphogenetic protein 10 (BMP10) complexed with extracellular domain of activin receptor-like kinase 1 (ALK1). Deposited 2019-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 317–424（108 aa）	Not recorded	NI NICKEL (II) ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17% PEG 3350, 0.175 M NH4I, 0.1 M HEPES pH 7.8	Resolution 2.80 Å R-free 0.279
6SF3 Bone morphogenetic protein 10 (BMP10) in complex with extracellular domain of activin receptor-like kinase 1 (ALK1) at 2.3 Angstrom Deposited 2019-07-31	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 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.07 M Amino acids (0.014 M DL-Glutamic acids monohydrate; 0.014 M DL-Alanine; 0.014 M Glycine; 0.014 M DL-Lysine monohydrochloride; 0.014 M DL-Serine), 0.07 M Buffer System 3 (0.07 M Tris(base)/BICINE), 35% Precipitant Mix 4 (9% v/v MPD, 9% w/v PEG 1000, 9% w/ PEG3350)	Resolution 2.30 Å R-free 0.243
7POI Prodomain bound BMP10 crystal form 1 Deposited 2021-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa） Chain C 22–316（295 aa） Chain D 22–316（295 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；294.15 K；19% PEG 3350 0.15 M Ammonium tartrate dibasic 0.02 M Sodium cacodylate trihydrate	Resolution 2.90 Å R-free 0.268
7POJ Prodomain bound BMP10 crystal form 2 Deposited 2021-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa） Chain C 22–316（295 aa） Chain D 22–316（295 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；294.15 K；20% PEG3350 0.2 M ammonium tartrate dibasic	Resolution 3.50 Å R-free 0.300
7PPA High resolution structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13	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 A 317–424（108 aa） Chain B 317–424（108 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294.15 K；14% PEG 3350 0.19 M Ammonium citrate dibasic 0.02 M Sodium citrate tribasic dihydrate	Resolution 1.48 Å R-free 0.207
7PPB 2.4 angstrom crystal structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13	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 A 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294.15 K；14% PEG 3350 0.14 M KCl	Resolution 2.40 Å R-free 0.235
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 317–424（108 aa） Chain D 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282

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

View Construct and Data Evidence

UniProt name	BMP10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–108； UniProt 320–424 Author chain B； PDBConstruct 4–108； UniProt 320–424

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	9dpy
Deposition date deposition_date	2024-09-23
最后修订 last_revision	2025-03-05
Structure title title	BMP-10 with BMP-9 Crystal Contacts
Keywords keywords	SIGNALING PROTEIN, BMP, bone morphogenetic protein, TGF-beta family; 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	20.36 Å
Radius of gyration Rg (electron density) rg_electron	20.34 Å
Forward intensity I(0) i0	12294600.00
Molecular weight molecular_weight	25006.0 kDa
Excluded volume excluded_volume	30780 Å³
Envelope volume envelope_volume	38015 Å³
Hydration-shell volume shell_volume	16707 Å³
Envelope diameter envelope_diameter	75.2 Å
Shell Rg shell_rg	25.53 Å
Envelope Rg envelope_rg	20.74 Å
Shape Rg shape_rg	20.39 Å
Total Rg total_rg	20.97 Å
Total atoms total_atoms	3394
Residues n_residues	210
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	74.1 Å
Rg (real space) rg_real	20.50 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	1.2290e+07
I(0) uncertainty (real space) i0_real_error	1.6350e+05
Rg (reciprocal space) rg_reciprocal	20.48 Å
I(0) (reciprocal space) i0_reciprocal	12290000.0000
Solution quality estimate total_estimate	0.5601
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.614
Kurtosis Kurtosis kurtosis	0.186
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1818000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.616; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.849; 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	Bone morphogenetic protein 10
Molecular weight formula_weight	12163.1 kDa
Mutation mutation	N357F, Y358F, A374T, Y409L, F411Y
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	3538

GDDGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCFFPLAEHLTPTKHAIIQTLVHLKNSQKASKACCVPTKLEPISILYLDKGVVTLKYKYEGMAVSECGCR

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 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	144

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8. Citations (1)

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Unit-cell length a length_a	42.752 Å
Unit-cell length b length_b	123.038 Å
Unit-cell length c length_c	120.558 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	61.520 Å
R factor r_factor	0.2165
R_work r_work	0.2141
R_free r_free	0.2512

fit	/app/data/saxs_computation/dp/9dpy/9dpy.fit
pddf	/app/data/pr_computation/dp/9dpy/9dpy.pr.out
profile	/app/data/saxs_computation/dp/9dpy/9dpy.dat

BMP-10 with BMP-9 Crystal Contacts

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

Bone morphogenetic protein 10

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