3kfd

Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily

Method: X-RAY DIFFRACTION

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

Transforming growth factor beta-1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	TGF-beta receptor type-2 × 2 （P37173） TGF-beta receptor type-1 × 2 （P36897） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	TGF-beta receptor type-2 × 2 （P37173） TGF-beta receptor type-1 × 2 （P36897） water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	TGF-beta receptor type-2 × 4 （P37173） TGF-beta receptor type-1 × 4 （P36897） water × 12	Consistent with protein count

Other States of the Same Protein in the Database

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 Author chain C； PDBConstruct 1–112； UniProt 279–390 Author chain D； PDBConstruct 1–112； UniProt 279–390

TGF-beta receptor type-2

Homo sapiens

UniProt P37173

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Transforming growth factor beta-1 × 2 （P01137） TGF-beta receptor type-1 × 2 （P36897） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transforming growth factor beta-1 × 2 （P01137） TGF-beta receptor type-1 × 2 （P36897） water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Transforming growth factor beta-1 × 4 （P01137） TGF-beta receptor type-1 × 4 （P36897） water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TGFR2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–116； UniProt 38–153 Author chain F； PDBConstruct 1–116； UniProt 38–153 Author chain G； PDBConstruct 1–116； UniProt 38–153 Author chain H； PDBConstruct 1–116； UniProt 38–153

TGF-beta receptor type-1

Homo sapiens

UniProt P36897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Transforming growth factor beta-1 × 2 （P01137） TGF-beta receptor type-2 × 2 （P37173） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transforming growth factor beta-1 × 2 （P01137） TGF-beta receptor type-2 × 2 （P37173） water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Transforming growth factor beta-1 × 4 （P01137） TGF-beta receptor type-2 × 4 （P37173） water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TGFR1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–85； UniProt 31–115 Author chain J； PDBConstruct 1–85； UniProt 31–115 Author chain K； PDBConstruct 1–85； UniProt 31–115 Author chain L； PDBConstruct 1–85； UniProt 31–115

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	3kfd
Deposition date deposition_date	2009-10-27
Structure title title	Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily
Keywords keywords	;TGF-beta, TGF-b1, TGF-beta receptor type-1, TGF-beta receptor type-2, TbRII, TbRI, Growth factor, Receptor, Serine/threonine-protein kinase, CYTOKINE-CYTOKINE RECEPTOR complex ;; CYTOKINE/CYTOKINE RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3kfd__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3kfd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kfd__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.68 Å
Rg (electron density)	35.29 Å
Total Rg	35.21 Å
Atom count	4527
Residues	574
Excluded volume	80653 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kfd__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3kfd__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3kfd__assembly_3__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Transforming growth factor beta-1
Molecular weight formula_weight	12809.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9151

ALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	TGF-beta receptor type-2
Molecular weight formula_weight	13225.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

VTDNNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	TGF-beta receptor type-1
Molecular weight formula_weight	9330.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L

ATALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSMCIAEIDLIPRDRPFVCAPSSKTGSVTTTYCCNQDHCNKIELPTTV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3kfda_
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

Domain ID domain_id	d3kfdb_
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

Domain ID domain_id	d3kfdc_
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

Domain ID domain_id	d3kfdd_
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

Domain ID domain_id	d3kfde_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

Domain ID domain_id	d3kfdf_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

Domain ID domain_id	d3kfdg_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

Domain ID domain_id	d3kfdh_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

CATH v4.4 (12 domains)

Domain ID domain_id	3kfdA00
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

Domain ID domain_id	3kfdB00
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

Domain ID domain_id	3kfdC00
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

Domain ID domain_id	3kfdD00
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

Domain ID domain_id	3kfdE00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3kfdF00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3kfdG00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3kfdH00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3kfdI00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3kfdJ00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3kfdK00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3kfdL00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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Unit-cell length a length_a	37.700 Å
Unit-cell length b length_b	99.350 Å
Unit-cell length c length_c	102.700 Å
Unit-cell angle α angle_alpha	64.01 °
Unit-cell angle β angle_beta	84.47 °
Unit-cell angle γ angle_gamma	84.34 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.995 Å
Low-resolution limit resolution_low	46.080 Å
R factor r_factor	0.2200
R_work r_work	0.2170
R_free r_free	0.2680

Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily

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

Transforming growth factor beta-1

State in the Current Structure

Other States of the Same Protein in the Database

TGF-beta receptor type-2

State in the Current Structure

Other States of the Same Protein in the Database

TGF-beta receptor type-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3kfd__assembly_1__model_1

3kfd__assembly_1__model_1 | I(q)

3kfd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily

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

Transforming growth factor beta-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TGF-beta receptor type-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TGF-beta receptor type-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3kfd__assembly_1__model_1

3kfd__assembly_1__model_1 | I(q)

3kfd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)