SAXSdb — 1tgk

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

TRANSFORMING GROWTH FACTOR BETA 3

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 301–412	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：PEG 4000	Resolution 3.30 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.

Other PDB	Difference from Current Entry 1TGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KTZ Crystal Structure of the Human TGF-beta Type II Receptor Extracellular Domain in Complex with TGF-beta3 Deposited 2002-01-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 301–412（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION USING A WELL SOLUTION CONTAINING 20% (V/V) 2-METHYL-2,4-PENTANEDIOL AND 0.1 M CITRATE PH 4.0	Resolution 2.15 Å R-free 0.215
1TGJ HUMAN TRANSFORMING GROWTH FACTOR-BETA 3, CRYSTALLIZED FROM DIOXANE Deposited 1996-07-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–412（112 aa）	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% (V/V) DIOXANE, 100 MM SODIUM ACETATE, PH 5.0	Resolution 2.00 Å
2PJY Structural basis for cooperative assembly of the TGF-beta signaling complex Deposited 2007-04-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 301–412（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10-20% PEG 3350, 0.4-0.65 M calcium acetate, 0.1-0.25M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.297
3EO1 Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3 Deposited 2008-09-26	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 C 301–412（112 aa） Fragment：UNP residues 301-412, receptor binding fragment Chain F 301–412（112 aa） Fragment：UNP residues 301-412, receptor binding fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；23% tert.-butanol, 0.1M sodium citrate, 0.2M phenoxyacetic acid, pH6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.279
3EO1 Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3 Deposited 2008-09-26	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 301–412（112 aa） Fragment：UNP residues 301-412, receptor binding fragment Chain L 301–412（112 aa） Fragment：UNP residues 301-412, receptor binding fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；23% tert.-butanol, 0.1M sodium citrate, 0.2M phenoxyacetic acid, pH6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.279
4UM9 Crystal structure of alpha V beta 6 with peptide Deposited 2014-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 259–269（11 aa） Fragment：RESIDUES 7-17	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 CA CALCIUM ION × 6 MG MAGNESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；15% PEG 4000, 0.1 M NACACODYLATE, PH 6.0	Resolution 2.50 Å R-free 0.266
4UM9 Crystal structure of alpha V beta 6 with peptide Deposited 2014-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 259–269（11 aa） Fragment：RESIDUES 7-17	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4 CA CALCIUM ION × 6 MG MAGNESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；15% PEG 4000, 0.1 M NACACODYLATE, PH 6.0	Resolution 2.50 Å R-free 0.266
8V52 Crystal structure of 2A10 Fab bound to Human TGF-beta3 Deposited 2023-11-30	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 301–412（112 aa） Chain B 301–412（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；25% PEG 1000, 0.1M HEPES pH 7.5	Resolution 2.50 Å R-free 0.269
8VS6 L-TGF-b3/avb8 Deposited 2024-01-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 24–412（389 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 5 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
8VSB L-TGF-b3/GARP Deposited 2024-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 24–412（389 aa） Chain B 24–412（389 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
9B9F Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII Deposited 2024-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 301–412（112 aa） Chain B 301–412（112 aa）	Mutation：R325E,Y390A,R394E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M lithium sulfate, 0.1 M tris pH 8.5, 30 %(w/v) polyethylene glycol 4000	Resolution 3.00 Å R-free 0.278
9B9F Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII Deposited 2024-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 301–412（112 aa） Chain G 301–412（112 aa）	Mutation：R325E,Y390A,R394E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M lithium sulfate, 0.1 M tris pH 8.5, 30 %(w/v) polyethylene glycol 4000	Resolution 3.00 Å R-free 0.278
9FK5 Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII Deposited 2024-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 301–412（112 aa） Chain B 301–412（112 aa）	Mutation：R325E,Y390A,R394E	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

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

View Construct and Data Evidence

UniProt name	TGFB3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 301–412

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	1tgk
Deposition date deposition_date	1996-07-10
Structure title title	HUMAN TRANSFORMING GROWTH FACTOR BETA 3, CRYSTALLIZED FROM PEG 4000
Keywords keywords	GROWTH FACTOR, MITOGEN, GLYCOPROTEIN; GROWTH FACTOR
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	18.13 Å
Radius of gyration Rg (electron density) rg_electron	18.23 Å
Forward intensity I(0) i0	3220320.00
Molecular weight molecular_weight	12722.0 kDa
Excluded volume excluded_volume	15807 Å³
Envelope volume envelope_volume	18750 Å³
Hydration-shell volume shell_volume	9870 Å³
Envelope diameter envelope_diameter	70.8 Å
Shell Rg shell_rg	21.79 Å
Envelope Rg envelope_rg	18.67 Å
Shape Rg shape_rg	18.29 Å
Total Rg total_rg	18.70 Å
Total atoms total_atoms	890
Residues n_residues	112
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	72.1 Å
Rg (real space) rg_real	18.43 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	3.2200e+06
I(0) uncertainty (real space) i0_real_error	4.5570e+04
Rg (reciprocal space) rg_reciprocal	18.39 Å
I(0) (reciprocal space) i0_reciprocal	3220000.0000
Solution quality estimate total_estimate	0.6060
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.6 Å
Skewness Skewness skewness	0.582
Kurtosis Kurtosis kurtosis	-0.158
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	364500.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.486; Stabil: 1.000; Sysdev: 0.408; Positv: 1.000; Valcen: 0.194; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1tgka_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (1 domains)

Domain ID domain_id	1tgkA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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8. Citations (2)

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Unit-cell length a length_a	77.800 Å
Unit-cell length b length_b	77.800 Å
Unit-cell length c length_c	143.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	—

Description description	TRANSFORMING GROWTH FACTOR BETA 3
Molecular weight formula_weight	12734.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	890

HUMAN TRANSFORMING GROWTH FACTOR BETA 3, CRYSTALLIZED FROM PEG 4000

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

TRANSFORMING GROWTH FACTOR BETA 3

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/tg/1tgk/1tgk.fit
pddf	/app/data/pr_computation/tg/1tgk/1tgk.pr.out
profile	/app/data/saxs_computation/tg/1tgk/1tgk.dat