2goo

Ternary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD

Method: X-RAY DIFFRACTION Dmax: 112.4 Å Quality: GOOD

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

Bone morphogenetic protein 2

Homo sapiens

UniProt P12643

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 283–396 Chain D; UniProt 283–396 Fragment:Residues 283-396 Bone morphogenetic protein receptor type IA × 2 (P36894) Activin receptor type 2A × 2 (P27038) 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

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.

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 D; PDBConstruct 1–114; UniProt 283–396

Bone morphogenetic protein receptor type IA

Homo sapiens

UniProt P36894

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 24–152 Chain E; UniProt 24–152 Fragment:Residues 24-152 Bone morphogenetic protein 2 × 2 (P12643) Activin receptor type 2A × 2 (P27038) 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

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.

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

View Construct and Data Evidence
UniProt name BMR1A_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–131; UniProt 24–152 Author chain E; PDBConstruct 3–131; UniProt 24–152

Activin receptor type 2A

Mus musculus

UniProt P27038

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 20–121 Chain F; UniProt 20–121 Fragment:Residues 20-121 Bone morphogenetic protein 2 × 2 (P12643) Bone morphogenetic protein receptor type IA × 2 (P36894) 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

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AVR2A_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–102; UniProt 20–121 Author chain F; PDBConstruct 1–102; UniProt 20–121

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2goo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2goo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2goo
Deposition date deposition_date2006-04-13
Structure title titleTernary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD
Keywords keywordsTGF-beta, BMP-2, BMPR-Ia, ActRII, ALK-3, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.35
Radius of gyration Rg (electron density) rg_electron35.38
Forward intensity I(0) i074569900.00
Molecular weight molecular_weight65091.0 kDa
Excluded volume excluded_volume79712 ų
Envelope volume envelope_volume120570 ų
Hydration-shell volume shell_volume29505 ų
Envelope diameter envelope_diameter121.0
Shell Rg shell_rg40.59
Envelope Rg envelope_rg34.11
Shape Rg shape_rg35.45
Total Rg total_rg35.59
Total atoms total_atoms4535
Residues n_residues565
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax112.4
Rg (real space) rg_real35.34
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real7.4570e+07
I(0) uncertainty (real space) i0_real_error1.1760e+06
Rg (reciprocal space) rg_reciprocal35.35
I(0) (reciprocal space) i0_reciprocal74570000.0000
Solution quality estimate total_estimate0.8568
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary52.4
Skewness Skewness skewness0.112
Kurtosis Kurtosis kurtosis-0.672
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5831000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.914; Smooth: 0.886

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2gooa_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.2 — Transforming growth factor (TGF)-beta
Domain ID domain_idd2goob_
Class classg — Small proteins
Fold Fold foldg.7 — Snake toxin-like
Superfamily Superfamily superfamilyg.7.1 — Snake toxin-like
Family Family familyg.7.1.3 — Extracellular domain of cell surface receptors
Domain ID domain_idd2gooc_
Class classg — Small proteins
Fold Fold foldg.7 — Snake toxin-like
Superfamily Superfamily superfamilyg.7.1 — Snake toxin-like
Family Family familyg.7.1.3 — Extracellular domain of cell surface receptors
Domain ID domain_idd2good_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.2 — Transforming growth factor (TGF)-beta
Domain ID domain_idd2gooe_
Class classg — Small proteins
Fold Fold foldg.7 — Snake toxin-like
Superfamily Superfamily superfamilyg.7.1 — Snake toxin-like
Family Family familyg.7.1.3 — Extracellular domain of cell surface receptors
Domain ID domain_idd2goof_
Class classg — Small proteins
Fold Fold foldg.7 — Snake toxin-like
Superfamily Superfamily superfamilyg.7.1 — Snake toxin-like
Family Family familyg.7.1.3 — Extracellular domain of cell surface receptors

CATH v4.4 (6 domains)

Domain ID domain_id2gooA00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id2gooB00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59
Domain ID domain_id2gooC00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59
Domain ID domain_id2gooD00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines
Domain ID domain_id2gooE00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59
Domain ID domain_id2gooF00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59

8. Citations (1)

9. Files and Curves (10)