SAXSdb — 3rf3

▼

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

Vinculin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Invasin ipaA × 1 （P18010） CACODYLATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Invasin ipaA × 1 （P18010） CACODYLATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Invasin ipaA × 2 （P18010） CACODYLATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VINC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 1–258 Author chain B； PDBConstruct 1–258； UniProt 1–258

Invasin ipaA

Shigella flexneri

UniProt P18010

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Vinculin × 1 （P18206） CACODYLATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Vinculin × 1 （P18206） CACODYLATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Vinculin × 2 （P18206） CACODYLATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPAA_SHIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–29； UniProt 488–512 Author chain D； PDBConstruct 5–29； UniProt 488–512

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	3rf3
Deposition date deposition_date	2011-04-05
Structure title title	Shigella IpaA-VBS3 in complex with human vinculin
Keywords keywords	;alpha-helix bundle domain, cytoskeletal protein, protein-protein interactions, cell adhesion, cytoskeleton, bacterial toxins, pathogen-host interactions, IpaA, Talin, F-actin, phosphatidylinositol 4 5-bisphosphate, Cytosol, Focal adhesion, protein binding-toxin complex ;; protein binding/toxin
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3rf3__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3rf3__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rf3__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.23 Å
Rg (electron density)	26.41 Å
Total Rg	26.72 Å
Atom count	4460
Residues	282
Excluded volume	39631 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rf3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rf3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3rf3__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Vinculin
Molecular weight formula_weight	28937.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9685

MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW

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 2 Entity 2 polymer

Description description	Invasin ipaA
Molecular weight formula_weight	3139.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GSHMTRETIFEASKKVTNSLSNLISLIGT

Source Source

Source organism organism	Shigella flexneri
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	804

▼

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3rf3a1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.9 — alpha-catenin/vinculin-like
Family Family family	a.24.9.1 — alpha-catenin/vinculin

Domain ID domain_id	d3rf3b1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.9 — alpha-catenin/vinculin-like
Family Family family	a.24.9.1 — alpha-catenin/vinculin

Domain ID domain_id	d3rf3b2
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.9 — alpha-catenin/vinculin-like
Family Family family	a.24.9.1 — alpha-catenin/vinculin

CATH v4.4 (4 domains)

Domain ID domain_id	3rf3A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	3rf3A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	3rf3B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	3rf3B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

▶

Unit-cell length a length_a	53.583 Å
Unit-cell length b length_b	85.319 Å
Unit-cell length c length_c	137.904 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.610 Å
Low-resolution limit resolution_low	53.000 Å
R factor r_factor	—
R_work r_work	0.1843
R_free r_free	0.1954

Shigella IpaA-VBS3 in complex with human vinculin

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

Vinculin

State in the Current Structure

Other States of the Same Protein in the Database

Invasin ipaA

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

3rf3__assembly_2__model_1

3rf3__assembly_2__model_1 | I(q)

3rf3__assembly_2__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Shigella IpaA-VBS3 in complex with human vinculin

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

Vinculin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Invasin ipaA

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

3rf3__assembly_2__model_1

3rf3__assembly_2__model_1 | I(q)

3rf3__assembly_2__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)