1E42: Ap-2 complex subunit beta

Beta2-adaptin appendage domain, from clathrin adaptor AP2. Determined by X-ray diffraction at 1.7 Å resolution. Released 21 Aug 2000.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 4,555
Mol. weight: 58.96 kDa
Ligands: NI, MG, DTD
Released: 21 Aug 2000

Explore 1E42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1E42 contains 17 α-helices and 38 β-strands across 2 chains. 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	709-711	3
β-strand	712-715	4	1
α-helix	717-719	3
β-strand	723-732	10	1
β-strand	735-744	10	1
β-strand	750	1	2
β-strand	754-757	4	3
β-strand	760	1	4
β-strand	765-766	2	1
β-strand	776	1	2
β-strand	781-789	9	1
β-strand	794	1	4
β-strand	802-808	7	3
β-strand	813-819	7	3
α-helix	822-825	4
β-strand	826	1	5
α-helix	834-843	10
α-helix	846-848	3
β-strand	850-854	5	6
α-helix	861-869	9
β-strand	874-881	8	6
β-strand	884-892	9	6
β-strand	893	1	5
β-strand	898-905	8	6
β-strand	912-918	7	6
α-helix	921-923	3
α-helix	924-935	12

Chain B: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	709-711	3
β-strand	712-715	4	7
α-helix	717-719	3
β-strand	723-732	10	7
β-strand	735-744	10	7
β-strand	750	1	8
β-strand	754-757	4	9
β-strand	760	1	10
β-strand	765-766	2	7
β-strand	776	1	8
β-strand	781-789	9	7
β-strand	794	1	10
β-strand	802-808	7	9
β-strand	813-819	7	9
α-helix	820-821	2
α-helix	822-825	4
β-strand	826	1	11
α-helix	834-843	10
α-helix	846-848	3
β-strand	850-854	5	12
α-helix	861-869	9
β-strand	874-881	8	12
β-strand	884-892	9	12
β-strand	893	1	11
β-strand	898-905	8	12
β-strand	912-918	7	12
α-helix	921-923	3
α-helix	924-935	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ap-2 complex subunit beta	A, B	protein	258	HOMO SAPIENS	P63010 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1E42_1 AP-2 COMPLEX SUBUNIT BETA (chains A, B)
MGSSHHHHHHSSGLVPRGSHMGMAPGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYME
MNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEP
LNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHL
NADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCR
APEVSQYIYQVYDSILKN

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1
MG	Magnesium ion	Mg	4
DTD	Dithiane diol	C4 H8 O2 S2	2

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

The Structure and Function of the Beta2-Adaptin Appendage Domain. Owen, D.J., Vallis, Y., Pearse, B.M.F. et al. EMBO J (2000) 19:4216. DOI 10.1093/EMBOJ/19.16.4216 · PubMed

Other PDB entries of the same protein (UniProt P63010 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2G30 1.6 Å, beta appendage of AP2 complexed with ARH peptide
5M5R 1.76 Å, Clathrin heavy chain N-terminal domain bound to beta2 adaptin clathrin box motif
2IV9 1.9 Å, B2-appendage from AP2 in complex with Eps15 peptide
6QH5 2.56 Å, AP2 clathrin adaptor mu2T156-phosphorylated core in closed conformation
2VGL 2.6 Å, AP2 clathrin adaptor core
4UQI 2.79 Å, AP2 controls clathrin polymerization with a membrane-activated switch
2IV8 2.8 Å, beta appendage in complex with b-arrestin peptide
7OHO 2.88 Å, Crystal structure of AP2 FCHO2 chimera
2JKR 2.98 Å, AP2 CLATHRIN ADAPTOR CORE with Dileucine peptide RM(phosphoS)QIKRLLSE
6URI 3.0 Å, HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex
2XA7 3.1 Å, AP2 clathrin adaptor core in active complex with cargo peptides
7OG1 3.25 Å, AP2 clathrin adaptor core in complex with cargo peptide and FCHO2

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