2yvc

Crystal structure of the Radixin FERM domain complexed with the NEP cytoplasmic tail

Method: X-RAY DIFFRACTION

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

Radixin

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Neprilysin × 1 （Q61391）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Neprilysin × 1 （Q61391）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Neprilysin × 1 （Q61391）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RADI_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–312； UniProt 1–310 Author chain B； PDBConstruct 3–312； UniProt 1–310 Author chain C； PDBConstruct 3–312； UniProt 1–310

Neprilysin

OrganismNot specified

UniProt Q61391

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Radixin × 1 （P26043）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Radixin × 1 （P26043）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Radixin × 1 （P26043）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEP_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–22； UniProt 2–23 Author chain E； PDBConstruct 1–22； UniProt 2–23 Author chain F； PDBConstruct 1–22； UniProt 2–23

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	2yvc
Deposition date deposition_date	2007-04-11
Structure title title	Crystal structure of the Radixin FERM domain complexed with the NEP cytoplasmic tail
Keywords keywords	Protein-peptide complex, CELL ADHESION; CELL ADHESION
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.

2yvc__assembly_1__model_1

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

Download this curve (.dat)

2yvc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yvc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.67 Å
Rg (electron density)	21.69 Å
Total Rg	22.66 Å
Atom count	2507
Residues	302
Excluded volume	44955 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yvc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yvc__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2yvc__assembly_3__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	Radixin
Molecular weight formula_weight	36924.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7607

GSMPKPINVRVTTMDAELEFAIQPNTTGKQLFDQVVKTVGLREVWFFGLQYVDSKGYSTWLKLNKKVTQQDVKKENPLQFKFRAKFFPEDVSEELIQEITQRLFFLQVKEAILNDEIYCPPETAVLLASYAVQAKYGDYNKEIHKPGYLANDRLLPQRVLEQHKLTKEQWEERIQNWHEEHRGMLREDSMMEYLKIAQDLEMYGVNYFEIKNKKGTELWLGVDALGLNIYEHDDKLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRILALCMGNHELYMRRRKPDTIEVQQMKAQAR

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Neprilysin
Molecular weight formula_weight	2533.9 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

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

GRSESQMDITDINAPKPKKKQR

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6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2yvca1
Class class	a — All alpha proteins
Fold Fold fold	a.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamily	a.11.2 — Second domain of FERM
Family Family family	a.11.2.1 — Second domain of FERM

Domain ID domain_id	d2yvca2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.5 — Third domain of FERM

Domain ID domain_id	d2yvca3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.4 — First domain of FERM

Domain ID domain_id	d2yvcb1
Class class	a — All alpha proteins
Fold Fold fold	a.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamily	a.11.2 — Second domain of FERM
Family Family family	a.11.2.1 — Second domain of FERM

Domain ID domain_id	d2yvcb2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.5 — Third domain of FERM

Domain ID domain_id	d2yvcb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.4 — First domain of FERM

Domain ID domain_id	d2yvcb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2yvcc1
Class class	a — All alpha proteins
Fold Fold fold	a.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamily	a.11.2 — Second domain of FERM
Family Family family	a.11.2.1 — Second domain of FERM

Domain ID domain_id	d2yvcc2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.5 — Third domain of FERM

Domain ID domain_id	d2yvcc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.4 — First domain of FERM

CATH v4.4 (9 domains)

Domain ID domain_id	2yvcA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2yvcA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2yvcA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	2yvcB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2yvcB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2yvcB03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	2yvcC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2yvcC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2yvcC03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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Unit-cell length a length_a	108.790 Å
Unit-cell length b length_b	116.838 Å
Unit-cell length c length_c	141.884 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	29.710 Å
R factor r_factor	0.2344
R_work r_work	0.2326
R_free r_free	0.2671

Crystal structure of the Radixin FERM domain complexed with the NEP cytoplasmic tail

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

Radixin

State in the Current Structure

Other States of the Same Protein in the Database

Neprilysin

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

2yvc__assembly_1__model_1

2yvc__assembly_1__model_1 | I(q)

2yvc__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (10 domains)

CATH v4.4 (9 domains)

7. Citations (4)

Crystal structure of the Radixin FERM domain complexed with the NEP cytoplasmic tail

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

Radixin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Neprilysin

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

2yvc__assembly_1__model_1

2yvc__assembly_1__model_1 | I(q)

2yvc__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (10 domains)

CATH v4.4 (9 domains)

7. Citations (4)