SAXSdb — 8dc0

▼

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

Transforming growth factor beta receptor type 3

Rattus norvegicus

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 A； UniProt 590–757	Fragment：ZPC domain (UNP residues 590-757)	Transforming growth factor beta-2 × 1 （P61812）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；13% PEG4000, 0.1 M trisodium citrate, 10% ethylene glycol	Resolution 1.93 Å R-free 0.257

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 8DC0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QW9 Crystal structure of betaglycan ZP-C domain Deposited 2011-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 591–763（173 aa） Fragment：unp residues 591-763 Chain B 591–763（173 aa） Fragment：unp residues 591-763	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；16-18% PEG 6000, 0.1 M Citrate, 0.9-1.0M LiCl2, pH 5.0, vapor diffusion, hanging drop, temperature 298K	Resolution 2.00 Å R-free 0.245
9FDY Betaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII Deposited 2024-05-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 31–360（330 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 590–757

Transforming growth factor beta-2

Homo sapiens

UniProt P61812

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 B； UniProt 303–414	Fragment：mmTGF-b2-7m2r (UNP residues 303-414)	Transforming growth factor beta receptor type 3 × 1 （P26342）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；13% PEG4000, 0.1 M trisodium citrate, 10% ethylene glycol	Resolution 1.93 Å R-free 0.257

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 8DC0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TFG AN UNUSUAL FEATURE REVEALED BY THE CRYSTAL STRUCTURE AT 2.2 ANGSTROMS RESOLUTION OF HUMAN TRANSFORMING GROWTH FACTOR-BETA2 Deposited 1992-11-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 303–414（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.95 Å
2TGI CRYSTAL STRUCTURE OF TRANSFORMING GROWTH FACTOR-BETA2: AN UNUSUAL FOLD FOR THE SUPERFAMILY Deposited 1993-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 303–414（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
4KXZ crystal structure of tgfb2 in complex with GC2008. Deposited 2013-05-28	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 303–414（112 aa） Fragment：unp residues 303-414 Chain B 303–414（112 aa） Fragment：unp residues 303-414	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；296 K；35% PEG400, 100mM MES, VAPOR DIFFUSION, temperature 296K, pH 6.0	Resolution 2.83 Å R-free 0.222
4KXZ crystal structure of tgfb2 in complex with GC2008. Deposited 2013-05-28	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 D 303–414（112 aa） Fragment：unp residues 303-414 Chain E 303–414（112 aa） Fragment：unp residues 303-414	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；296 K；35% PEG400, 100mM MES, VAPOR DIFFUSION, temperature 296K, pH 6.0	Resolution 2.83 Å R-free 0.222
5TX4 Derivative of mouse TGF-beta2, with a deletion of residues 52-71 and K25R, R26K, L51R, A74K, C77S, L89V, I92V, K94R T95K, I98V single amino acid substitutions, bound to human TGF-beta type II receptor ectodomain residues 15-130 Deposited 2016-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 303–414（112 aa） Fragment：UNP residues 303-414	Mutation：deletion of residues 52-71 and K25R, R26K, L51R, A74K, C77S, L89V, I92V, K94R T95K, I98V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Hepes, pH 7.5, 60 % v/v (+/-)-2-Methyl-2,4-pentanediol	Resolution 1.88 Å R-free 0.222
6I9J Human transforming growth factor beta2 in a tetragonal crystal form Deposited 2018-11-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 331–442（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；20% isopropanol, 0.2M calcium chloride, 0.1M sodium acetate pH 4.6	Resolution 2.00 Å R-free 0.253
6XM2 The structure of the 4A11.v7 antibody in complex with human TGFb2 Deposited 2020-06-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain K 303–414（112 aa） Fragment：mature domain Chain L 303–414（112 aa） Fragment：mature domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20% PEG 1000, 0.1 M Tris pH8.5	Resolution 1.91 Å R-free 0.244
6XM2 The structure of the 4A11.v7 antibody in complex with human TGFb2 Deposited 2020-06-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 303–414（112 aa） Fragment：mature domain Chain J 303–414（112 aa） Fragment：mature domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20% PEG 1000, 0.1 M Tris pH8.5	Resolution 1.91 Å R-free 0.244
7RCO Crystal structure of human TGF-beta-2 bound to 4A11.V2 Fab Deposited 2021-07-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 303–414（112 aa） Fragment：mature domain (UNP residues 303-414) Chain B 303–414（112 aa） Fragment：mature domain (UNP residues 303-414)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；15% PEG4000, 0.1 M sodium cacodylate, pH 6.0	Resolution 2.90 Å R-free 0.286
8FXS Crystal structure of human pro-TGF-beta2 in complex with Nb9 Deposited 2023-01-25	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 21–414（394 aa） Chain B 21–414（394 aa）	Mutation：C24S, N140R, R298_R303delinsG Mutation：C24S, N140R, R298_R303delinsG	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Crystals of the Nb9/proTGF-beta2 complex (1 microliter) were formed in hanging drops with 1 microliter of 100 mM HEPES pH 7.6, 10% PEG 4000.	Resolution 3.15 Å R-free 0.301
8FXV Crystal structure of human proTGF-beta2 in complex with Nb18 Deposited 2023-01-25	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 21–414（394 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Crystals of the Nb18/proTGF-beta2 complex (1 microliter) were formed in hanging drops with 1 microliter of 100 mM HEPES pH 7.4, 26.7% Jeffamine ED2001.	Resolution 2.20 Å R-free 0.249

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TGFB2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–112； UniProt 303–414

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8dc0
Deposition date deposition_date	2022-06-15
Structure title title	Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini monomer TGFb2 (mmTGF-b2-7M2R)
Keywords keywords	Complex, Betaglycan, TGFb2, CYTOKINE; CYTOKINE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	23.34 Å
Radius of gyration Rg (electron density) rg_electron	22.49 Å
Forward intensity I(0) i0	14710500.00
Molecular weight molecular_weight	29190.0 kDa
Excluded volume excluded_volume	36701 Å³
Envelope volume envelope_volume	46360 Å³
Hydration-shell volume shell_volume	18744 Å³
Envelope diameter envelope_diameter	84.7 Å
Shell Rg shell_rg	27.44 Å
Envelope Rg envelope_rg	23.01 Å
Shape Rg shape_rg	22.47 Å
Total Rg total_rg	23.26 Å
Total atoms total_atoms	2046
Residues n_residues	255
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

▼

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

Maximum dimension Dmax dmax	79.3 Å
Rg (real space) rg_real	23.53 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	1.4710e+07
I(0) uncertainty (real space) i0_real_error	2.3380e+05
Rg (reciprocal space) rg_reciprocal	23.49 Å
I(0) (reciprocal space) i0_reciprocal	14710000.0000
Solution quality estimate total_estimate	0.7814
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.525
Kurtosis Kurtosis kurtosis	-0.267
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1959000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.812; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Transforming growth factor beta receptor type 3
Molecular weight formula_weight	19915.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2131

GNATFNMELYNTDLFLVPSPGVFSVAENEHVYVEVSVTKADQDLGFAIQTCFLSPYSNPDRMSDYTIIENICPKDDSVKFYSSKRVHFPIPHAEVDKKRFSFLFKSVFNTSLLFLHCELTLCSRKKGSLKLPRCVTPDDACTSLDATMIWTMMQNKKTFTKPLAVVLQHHHHHH

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Transforming growth factor beta-2
Molecular weight formula_weight	12944.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ALDAAYCFRNVQDNCCLRPLYIDFRKDLGWKWIHEPKGYNANFCAGACPYLWSSDTQHSRVLSLYNTINPRASKSPRCRSQDLEPLTIVYYVGRKPKVEQLSNMIVKSCKCS

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	85

▶

8. Citations (1)

▶

Unit-cell length a length_a	76.456 Å
Unit-cell length b length_b	90.453 Å
Unit-cell length c length_c	98.872 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	66.740 Å
R factor r_factor	0.2215
R_work r_work	0.2186
R_free r_free	0.2566

fit	/app/data/saxs_computation/dc/8dc0/8dc0.fit
pddf	/app/data/pr_computation/dc/8dc0/8dc0.pr.out
profile	/app/data/saxs_computation/dc/8dc0/8dc0.dat

Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini monomer TGFb2 (mmTGF-b2-7M2R)

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

Transforming growth factor beta receptor type 3

State in the Current Structure

Other States of the Same Protein in the Database

Transforming growth factor beta-2

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)