9fdy

Betaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII

Method: ELECTRON MICROSCOPY Dmax: 130.0 Å Quality: GOOD

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

Transforming growth factor beta-1

Homo sapiens

UniProt P01137

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 279–390 Chain B; UniProt 279–390 Fragment:Mature Transforming growth factor beta receptor type 3 × 1 (P26342) TGF-beta receptor type-2 × 2 (P37173) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 Å

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.

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TGFB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–112; UniProt 279–390 Author chain B; PDBConstruct 1–112; UniProt 279–390

Transforming growth factor beta receptor type 3

Rattus norvegicus

UniProt P26342

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 31–360 Not recorded Transforming growth factor beta-1 × 2 (P01137) TGF-beta receptor type-2 × 2 (P37173) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 Å

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 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TGBR3_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 4–333; UniProt 31–360

TGF-beta receptor type-2

Homo sapiens

UniProt P37173

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 42–153 Chain E; UniProt 42–153 Not recorded Transforming growth factor beta-1 × 2 (P01137) Transforming growth factor beta receptor type 3 × 1 (P26342) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 Å

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.

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TGFR2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 2–113; UniProt 42–153 Author chain E; PDBConstruct 2–113; UniProt 42–153

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 9fdy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9fdy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9fdy
Deposition date deposition_date2024-05-17
最后修订 last_revision2025-03-12
Structure title titleBetaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII
Keywords keywordsComplex, Betaglycan, TGFBR3, TGFb1, TGFBR2, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.10
Radius of gyration Rg (electron density) rg_electron36.10
Forward intensity I(0) i0121782000.00
Molecular weight molecular_weight87397.0 kDa
Excluded volume excluded_volume109100 ų
Envelope volume envelope_volume149570 ų
Hydration-shell volume shell_volume37865 ų
Envelope diameter envelope_diameter136.9
Shell Rg shell_rg38.15
Envelope Rg envelope_rg36.53
Shape Rg shape_rg36.10
Total Rg total_rg36.25
Total atoms total_atoms6119
Residues n_residues770
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 dmax130.0
Rg (real space) rg_real36.52
Rg uncertainty (real space) rg_real_error1.53
I(0) (real space) i0_real1.2180e+08
I(0) uncertainty (real space) i0_real_error2.3800e+06
Rg (reciprocal space) rg_reciprocal36.26
I(0) (reciprocal space) i0_reciprocal121800000.0000
Solution quality estimate total_estimate0.8126
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.4
Skewness Skewness skewness0.644
Kurtosis Kurtosis kurtosis0.032
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9462000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.742; Smooth: 0.823

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)