SAXSdb — 8fxv

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

Transforming growth factor beta-2 proprotein

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 21–414	Not recorded	Nanobody clone 18 × 2 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

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 8FXV	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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：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
8DC0 Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini monomer TGFb2 (mmTGF-b2-7M2R) Deposited 2022-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 303–414（112 aa） Fragment：mmTGF-b2-7m2r (UNP residues 303-414)	Not recorded	No recorded non-water small molecule	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
8FXS Crystal structure of human pro-TGF-beta2 in complex with Nb9 Deposited 2023-01-25	Different construct Different mutation/modification 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

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–393； UniProt 21–414

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8fxv
Deposition date deposition_date	2023-01-25
Structure title title	Crystal structure of human proTGF-beta2 in complex with Nb18
Keywords keywords	TGF-b TGF-beta nanobody latent procomplex prodomain, CYTOKINE; CYTOKINE
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	30.57 Å
Radius of gyration Rg (electron density) rg_electron	30.45 Å
Forward intensity I(0) i0	40321000.00
Molecular weight molecular_weight	49472.0 kDa
Excluded volume excluded_volume	62019 Å³
Envelope volume envelope_volume	86573 Å³
Hydration-shell volume shell_volume	26463 Å³
Envelope diameter envelope_diameter	111.2 Å
Shell Rg shell_rg	33.94 Å
Envelope Rg envelope_rg	30.18 Å
Shape Rg shape_rg	30.42 Å
Total Rg total_rg	30.92 Å
Total atoms total_atoms	6895
Residues n_residues	434
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	104.7 Å
Rg (real space) rg_real	30.82 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	4.0320e+07
I(0) uncertainty (real space) i0_real_error	6.1510e+05
Rg (reciprocal space) rg_reciprocal	30.72 Å
I(0) (reciprocal space) i0_reciprocal	40320000.0000
Solution quality estimate total_estimate	0.8576
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.2 Å
Skewness Skewness skewness	0.479
Kurtosis Kurtosis kurtosis	-0.351
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3275000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.754; Smooth: 0.850

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Transforming growth factor beta-2 proprotein
Molecular weight formula_weight	45195.4 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	6958

GPSLSTSSTLDMDQFMRKRIEAIRGQILSKLKLTSPPEDYPEPEEVPPEVISIYNSTRDLLQEKASRRAAACERERSDEEYYAKEVYKIDMPPFFPSENAIPPTFYRPYFRIVRFDVSAMEKRASNLVKAEFRVFRLQNPKARVPEQRIELYQILKSKDLTSPTQRYIDSKVVKTRAEGEWLSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVPSNNYIIPNKSEELEARFAGIDGTSTYTSGDQKTIKSTRKKNSGKTPHLLLMLLPSYRLESQQTNGALDAAYCFRNVQDNCCLRPLYIDFKRDLGWKWIHEPKGYNANFCAGACPYLWSSDTQHSRVLSLYNTINPEASASPCCVSQDLEPLTILYYIGKTPKIEQLSNMIVKSCKCS

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Nanobody clone 18
Molecular weight formula_weight	13519.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLQESGGGLVQAGGSLRLSCAASGYISNDDVMGWYRQAPGKEREFVAAISVGASTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAQSEGGYWFGYWGQGTQVTVSSHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8fxvB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	70.750 Å
Unit-cell length b length_b	78.160 Å
Unit-cell length c length_c	88.890 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	4

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	45.170 Å
R factor r_factor	0.2279
R_work r_work	0.2268
R_free r_free	0.2491

fit	/app/data/saxs_computation/fx/8fxv/8fxv.fit
pddf	/app/data/pr_computation/fx/8fxv/8fxv.pr.out
profile	/app/data/saxs_computation/fx/8fxv/8fxv.dat

Crystal structure of human proTGF-beta2 in complex with Nb18

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

Transforming growth factor beta-2 proprotein

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 (4)

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 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)