1w80

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170

Method: X-RAY DIFFRACTION

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

ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT

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） SYNAPTOJANIN 1 × 1 （O43426） BENZAMIDINE × 1 CARBONATE ION × 3 DITHIANE DIOL × 1 SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A2A2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–250； UniProt 695–938

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	ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT × 1 （P17427） BENZAMIDINE × 1 CARBONATE ION × 3 DITHIANE DIOL × 1 SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYJ1_HUMAN
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain P； PDBConstruct 1–12； UniProt 1479–1490 Author chain Q； PDBConstruct 1–12； UniProt 1460–1471

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	1w80
Deposition date deposition_date	2004-09-14
Structure title title	Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170
Keywords keywords	;ENDOCYTOSIS/EXOCYTOSIS, ENDOCYTOSIS, ALPHA-ADAPTIN APPENDAGE, ADAPTOR COMPLEX, AP2, SYNAPTOJANIN, EXOCYTOSIS, LIPID-BINDING, ENDOCYTOSIS-EXOCYTOSIS complex ;; ENDOCYTOSIS/EXOCYTOSIS
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.

1w80__assembly_1__model_1

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

Download this curve (.dat)

1w80__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w80__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.59 Å
Rg (electron density)	20.62 Å
Total Rg	21.38 Å
Atom count	2130
Residues	264
Excluded volume	37953 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w80__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	ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT
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	2439

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
EC 编号 ec_number	3.1.3.36
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	SYNAPTOJANIN 1
Molecular weight formula_weight	1342.4 kDa
EC 编号 ec_number	3.1.3.36
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

LDGFKDSFDLQG

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	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	277

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1w80a1
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	d1w80a2
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

Domain ID domain_id	d1w80a3
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

CATH v4.4 (2 domains)

Domain ID domain_id	1w80A01
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	1w80A02
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	146.599 Å
Unit-cell length b length_b	67.322 Å
Unit-cell length c length_c	39.721 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.53 °
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	1.900 Å
Low-resolution limit resolution_low	72.550 Å
R factor r_factor	0.1790
R_work r_work	0.1770
R_free r_free	0.2240

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170

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

ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1w80__assembly_1__model_1

1w80__assembly_1__model_1 | I(q)

1w80__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170

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

ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1w80__assembly_1__model_1

1w80__assembly_1__model_1 | I(q)

1w80__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)