SAXSdb — 9d20

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

Activin receptor type-2B

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 25–118	Not recorded	Protein delta homolog 1 × 1 （P80370） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 3 FUC alpha-L-fucopyranose × 1 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2.1 M (NH4)2SO4, 0.1 M HEPES PH 7.6 and 2.5% polyethylene glycol (PEG) 400	Resolution 2.67 Å R-free 0.242
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 25–118	Not recorded	Protein delta homolog 1 × 1 （P80370） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 FUC alpha-L-fucopyranose × 1 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2.1 M (NH4)2SO4, 0.1 M HEPES PH 7.6 and 2.5% polyethylene glycol (PEG) 400	Resolution 2.67 Å R-free 0.242

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 9D20	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QLU Crystal structure of Activin receptor type II kinase domain from human Deposited 2007-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 190–487（298 aa） Fragment：Protein kinase domain	Not recorded	SO4 SULFATE ION × 2 ADE ADENINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；45mM MES, 90mM ammonium sulfate, 11% polyethylene glycol monomethyl ether 5000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.283
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	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 E 19–134（116 aa） Fragment：Extracellular domain Chain F 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	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 K 19–134（116 aa） Fragment：Extracellular domain Chain L 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain Q 19–134（116 aa） Fragment：Extracellular domain Chain R 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain W 19–134（116 aa） Fragment：Extracellular domain Chain X 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain e 19–134（116 aa） Fragment：Extracellular domain Chain f 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain k 19–134（116 aa） Fragment：Extracellular domain Chain l 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
5NGV CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, ORTHORHOMBIC CRYSTAL FORM Deposited 2017-03-20	Different construct 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 24–117（94 aa） Fragment：LIGAND BINDING domain	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；293 K；0.1M PHOSPHATE-CITRATE, 40% PEG 300	Resolution 2.00 Å R-free 0.198
5NHR CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, CUBIC CRYSTAL FORM Deposited 2017-03-22	Different construct 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 24–117（94 aa） Fragment：VL, UNP residues 24-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；1.4M AMMONIUM SULFATE, 0.1M SODIUM CITRATE	Resolution 3.35 Å R-free 0.229
5NHR CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, CUBIC CRYSTAL FORM Deposited 2017-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 24–117（94 aa） Fragment：VL, UNP residues 24-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；1.4M AMMONIUM SULFATE, 0.1M SODIUM CITRATE	Resolution 3.35 Å R-free 0.229
7MRZ Structure of GDF11 bound to fused ActRIIB-ECD and Alk4-ECD with Anti-ActRIIB Fab fragment Deposited 2021-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain C 19–134（116 aa） Fragment：Extracellular domains of both proteins in the fused construct	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 0.9M ammonium sulfate, 0.9 M KCl	Resolution 3.00 Å R-free 0.327
7OLY Structure of activin A in complex with an ActRIIB-Alk4 fusion reveal insight into activin receptor interactions Deposited 2021-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain C 19–134（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；17.7 mg/ml complex in 20 mM HEPES, 200 mM NaCl pH 7.5. 100 + 100 nl sitting drop in a MRC 3-well plate with reservoir 0.1 M Na cacodylate pH 6.5 and 17 % (w/v) PEG 4000).	Resolution 3.27 Å R-free 0.269
9N4K CryoEM structure of ALK2-ActRIIB bound to BMP6 Deposited 2025-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 19–134（116 aa） Chain F 19–134（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 BMA beta-D-mannopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50mM Tris-HCL, 100mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

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

View Construct and Data Evidence

UniProt name	AVR2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 25–118 Author chain E； PDBConstruct 1–94； UniProt 25–118

Protein delta homolog 1

Homo sapiens

UniProt P80370

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 171–251	Not recorded	Activin receptor type-2B × 1 （Q13705） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 3 FUC alpha-L-fucopyranose × 1 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2.1 M (NH4)2SO4, 0.1 M HEPES PH 7.6 and 2.5% polyethylene glycol (PEG) 400	Resolution 2.67 Å R-free 0.242
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 171–251	Not recorded	Activin receptor type-2B × 1 （Q13705） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 FUC alpha-L-fucopyranose × 1 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2.1 M (NH4)2SO4, 0.1 M HEPES PH 7.6 and 2.5% polyethylene glycol (PEG) 400	Resolution 2.67 Å R-free 0.242

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	DLK1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–81； UniProt 171–251 Author chain D； PDBConstruct 1–81； UniProt 171–251

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	9d20
Deposition date deposition_date	2024-08-08
Structure title title	Crystal structure of DLK1 in complex with ACVR2B
Keywords keywords	DLK1, ACVR2B, Complex, SIGNALING, 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	24.97 Å
Radius of gyration Rg (electron density) rg_electron	24.54 Å
Forward intensity I(0) i0	34821200.00
Molecular weight molecular_weight	39997.0 kDa
Excluded volume excluded_volume	47756 Å³
Envelope volume envelope_volume	65614 Å³
Hydration-shell volume shell_volume	23070 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	30.62 Å
Envelope Rg envelope_rg	24.51 Å
Shape Rg shape_rg	24.56 Å
Total Rg total_rg	25.19 Å
Total atoms total_atoms	2764
Residues n_residues	346
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	84.0 Å
Rg (real space) rg_real	24.95 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	3.4820e+07
I(0) uncertainty (real space) i0_real_error	5.3010e+05
Rg (reciprocal space) rg_reciprocal	24.96 Å
I(0) (reciprocal space) i0_reciprocal	34820000.0000
Solution quality estimate total_estimate	0.8949
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.0 Å
Skewness Skewness skewness	0.276
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1770000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Activin receptor type-2B
Molecular weight formula_weight	11219.3 kDa
EC 编号 ec_number	2.7.11.30
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A
Atom count atom_count	2776

ETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPE

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Protein delta homolog 1
Molecular weight formula_weight	8619.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ANSCTPNPCENDGVCTDIGGDFRCRCPAGFIDKTCSRPVTNCASSPCQNGGTCLQHTQVSYECLCKPEFTGLTCVKKRALS

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	Trichoplusia ni

Entity 3 Entity 3 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	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	man
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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8. Citations (1)

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Unit-cell length a length_a	120.980 Å
Unit-cell length b length_b	52.970 Å
Unit-cell length c length_c	97.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.673 Å
Low-resolution limit resolution_low	35.888 Å
R factor r_factor	0.2139
R_work r_work	0.2124
R_free r_free	0.2416

fit	/app/data/saxs_computation/d2/9d20/9d20.fit
pddf	/app/data/pr_computation/d2/9d20/9d20.pr.out
profile	/app/data/saxs_computation/d2/9d20/9d20.dat

Crystal structure of DLK1 in complex with ACVR2B

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

Activin receptor type-2B

State in the Current Structure

Other States of the Same Protein in the Database

Protein delta homolog 1

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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)