1W80: PDB entry 1W80

Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170. Determined by X-ray diffraction at 1.9 Å resolution. Released 27 Oct 2004.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: MUS MUSCULUS, HOMO SAPIENS
Chains: 3
Atoms: 2,439
Mol. weight: 31.4 kDa
Ligands: DTD, CO3, BEN
Released: 27 Oct 2004

Explore 1W80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1W80 contains 10 α-helices and 15 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	695-698	4
α-helix	701-706	6
β-strand	713-718	6	1
β-strand	722-731	10	1
β-strand	734-743	10	1
β-strand	749-757	9	2
α-helix	760-765	6
β-strand	766-769	4	1
α-helix	772-774	3
β-strand	777	1	2
β-strand	782-791	10	1
β-strand	800-807	8	2
β-strand	810-817	8	2
α-helix	822-825	4
β-strand	826-828	3	3
α-helix	833-842	10
α-helix	846-848	3
β-strand	849-855	7	3
α-helix	862-872	11
α-helix	874	1
β-strand	875-877	3	3
β-strand	887-894	8	3
β-strand	899-909	11	3
β-strand	914-921	8	3
α-helix	924-935	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adapter-related protein complex 2 alpha 2 subunit	A	protein	250	MUS MUSCULUS	P17427 (AlphaFold model)
Synaptojanin 1	P	protein	12	HOMO SAPIENS	O43426 (AlphaFold model)
Synaptojanin 1	Q	protein	12	HOMO SAPIENS	O43426 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1W80_1 ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT (chains A)
GSPGILAPLAPGSEDNFARFVCKNNGVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTSTQ
FLNFTPTLICADDLQTNLNLQTKPVDPTVDGGAQVQQVINIECISDFTEAPVLNIQFRYG
GTFQNVSVKLPITLNKFFQPTEMASQDFFQRWKQLSNPQQEVQNIFKAKHPMDTEITKAK
IIGFGSALLEEVDPNPANFVGAGIIHTKTTQIGCLLRLEPNLQAQMYRLTLRTSKDTVSQ
RLCELLSEQF

Sequence of entity 2 (P), FASTA

>1W80_2 SYNAPTOJANIN 1 (chains P)
NPKGWVTFEEEE

Sequence of entity 3 (Q), FASTA

>1W80_3 SYNAPTOJANIN 1 (chains Q)
LDGFKDSFDLQG

Ligands and cofactors

ID	Name	Formula	Copies
DTD	Dithiane diol	C4 H8 O2 S2	1
CO3	Carbonate ion	C O3	3
BEN	Benzamidine	C7 H8 N2	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Evolving Nature of the Ap2 Alpha-Appendage Hub During Clathrin-Coated Vesicle Endocytosis. Praefcke, G.J.K., Ford, M.G.J., Schmid, E.M. et al. EMBO J (2004) 23:4371. DOI 10.1038/SJ.EMBOJ.7600445 · PubMed

Other PDB entries of the same protein (UniProt P17427 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KYF 1.22 Å, Ap-2 clathrin adaptor alpha-appendage in complex with EPS15 dpf peptide
1QTS 1.4 Å, Crystal structure of the ap-2 clathrin adaptor alpha-appendage
7OHI 1.41 Å, FCHO1-peptide-AP2 alpha ear complex
1QTP 1.6 Å, Crystal structure of the ap-2 clathrin adaptor alpha-appendage
2VJ0 1.6 Å, Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex,…
1KYU 1.8 Å, Ap-2 clathrin adaptor alpha-appendage in complex with EPS15 dpf peptide
1B9K 1.9 Å, Alpha-adaptin appendage domain, from clathrin adaptor AP2
3HS8 1.9 Å, Intersectin 1-peptide-AP2 alpha ear complex
9PUE 1.91 Å, Structure of Alpha Appendage of AP2 bound to the FxDxF motif derived of CCDC32
1KY6 2.0 Å, Ap-2 clathrin adaptor alpha-appendage in complex with epsin dpw peptide
1KYD 2.0 Å, Ap-2 clathrin adaptor alpha-appendage in complex with epsin dpw peptide
9PPP 2.1 Å, Structure of Alpha Appendage of AP2 bound to the extended FxDxF motif derived of CCDC32

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