2vj0

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170

Method: X-RAY DIFFRACTION

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

AP-2 COMPLEX SUBUNIT ALPHA-2

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SYNAPTOJANIN-1 × 1 （O43426） AMPHIPHYSIN × 1 （O08838） BENZAMIDINE × 1 DITHIANE DIOL × 1 SULFATE ION × 3 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AP2A2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–250； UniProt 693–938

SYNAPTOJANIN-1

OrganismNot specified

UniProt O43426

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） AMPHIPHYSIN × 1 （O08838） BENZAMIDINE × 1 DITHIANE DIOL × 1 SULFATE ION × 3 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYNJ1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–12； UniProt 1479–1490

AMPHIPHYSIN

OrganismNot specified

UniProt O08838

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	AP-2 COMPLEX SUBUNIT ALPHA-2 × 1 （P17427） SYNAPTOJANIN-1 × 1 （O43426） BENZAMIDINE × 1 DITHIANE DIOL × 1 SULFATE ION × 3 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMPH_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Q； PDBConstruct 1–7； UniProt 324–330

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	2vj0
Deposition date deposition_date	2007-12-06
Structure title title	Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170
Keywords keywords	;PROTEIN TRANSPORT, CYTOPLASMIC VESICLE, ALTERNATIVE SPLICING, TRANSPORT, COATED PIT, SH3 DOMAIN, ENDOCYTOSIS, ALPHA-ADAPTIN, GOLGI APPARATUS, PHOSPHORYLATION, AP2, SYNAPSE, MEMBRANE, CYTOPLASM, COILED COIL, AMPHIPHYSIN, CYTOSKELETON, SYNAPTOJANIN, LIPID-BINDING, CELL JUNCTION ;; PROTEIN TRANSPORT
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.

2vj0__assembly_1__model_1

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

Download this curve (.dat)

2vj0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vj0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.35 Å
Rg (electron density)	20.41 Å
Total Rg	21.16 Å
Atom count	2101
Residues	261
Excluded volume	37483 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vj0__assembly_1__model_1`	trimeric （3）	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 (8)

Entity 1 Entity 1 polymer

Description description	AP-2 COMPLEX SUBUNIT ALPHA-2
Molecular weight formula_weight	28048.0 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	2463

GSPGILAPLAPGSEDNFARFVCKNNGVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTSTQFLNFTPTLICADDLQTNLNLQTKPVDPTVDGGAQVQQVINIECISDFTEAPVLNIQFRYGGTFQNVSVKLPITLNKFFQPTEMASQDFFQRWKQLSNPQQEVQNIFKAKHPMDTEITKAKIIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQRLCELLSEQF

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	SYNAPTOJANIN-1
Molecular weight formula_weight	1465.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

NPKGWVTFEEEE

Entity 3 Entity 3 polymer

Description description	AMPHIPHYSIN
Molecular weight formula_weight	866.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

FEDNFVP

Entity 4 Entity 4 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DITHIANE DIOL
Molecular weight formula_weight	152.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vj0a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.10 — Clathrin adaptor appendage domain
Family Family family	b.1.10.1 — Alpha-adaptin ear subdomain-like

Domain ID domain_id	d2vj0a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.105 — Subdomain of clathrin and coatomer appendage domain
Superfamily Superfamily superfamily	d.105.1 — Subdomain of clathrin and coatomer appendage domain
Family Family family	d.105.1.1 — Clathrin adaptor appendage, alpha and beta chain-specific domain

CATH v4.4 (2 domains)

Domain ID domain_id	2vj0A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1230 — Gamma-adaptin ear (GAE) domain

Domain ID domain_id	2vj0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

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Unit-cell length a length_a	144.508 Å
Unit-cell length b length_b	66.980 Å
Unit-cell length c length_c	39.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	17.760 Å
R factor r_factor	0.1820
R_work r_work	0.1810
R_free r_free	0.2080

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170

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

AP-2 COMPLEX SUBUNIT ALPHA-2

State in the Current Structure

Other States of the Same Protein in the Database

SYNAPTOJANIN-1

State in the Current Structure

Other States of the Same Protein in the Database

AMPHIPHYSIN

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

2vj0__assembly_1__model_1

2vj0__assembly_1__model_1 | I(q)

2vj0__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170

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

AP-2 COMPLEX SUBUNIT ALPHA-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

SYNAPTOJANIN-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

AMPHIPHYSIN

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

2vj0__assembly_1__model_1

2vj0__assembly_1__model_1 | I(q)

2vj0__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)