4AFI: PDB entry 4AFI

Complex between Vamp7 longin domain and fragment of delta-adaptin from AP3. Determined by X-ray diffraction at 2.8 Å resolution. Released 30 May 2012.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: HOMO SAPIENS, MUS MUSCULUS
Chains: 2
Atoms: 2,445
Mol. weight: 39.39 kDa
Ligands: PR
Released: 30 May 2012

Explore 4AFI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4AFI contains 9 α-helices and 14 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	1
β-strand	47-49	3	2
β-strand	56-63	8	3
β-strand	66-72	7	3
α-helix	78-86	9
β-strand	94-100	7	3
β-strand	103-110	8	3
β-strand	113-120	8	3
α-helix	125-143	19
α-helix	144-148	5
α-helix	150-151	2
α-helix	156-172	17

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	3
β-strand	47-49	3	2
β-strand	56-63	8	1
β-strand	66-72	7	1
α-helix	78-86	9
β-strand	94-100	7	1
β-strand	103-110	8	1
β-strand	113-120	8	1
α-helix	125-143	19
α-helix	144-148	5
α-helix	156-171	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ap-3 complex subunit delta-1, vesicle-associated membrane protein 7	A, B	protein	173	HOMO SAPIENS, MUS MUSCULUS	O14617 (AlphaFold model), P70280 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4AFI_1 AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 (chains A, B)
GSPFYIKSSPSPQKRYQDTPGVEHIPVVQIDLSVPLKVPGLPMSDQYVKLEEAMAILFAV
VARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITD
DDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSEN

Ligands and cofactors

ID	Name	Formula	Copies
PR	Praseodymium ion	Pr	2

Primary citation

Structural Basis of the Intracellular Sorting of the Snare Vamp7 by the Ap3 Adaptor Complex. Kent, H.M., Evans, P.R., Schaefer, I.B. et al. Dev Cell (2012) 22:979. DOI 10.1016/J.DEVCEL.2012.01.018 · PubMed

Other PDB entries of the same protein (UniProt O14617 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9C5C 3.6 Å, Structure of Human Adaptor Protein Complex AP-3 in the Apo State
9C59 4.3 Å, Human AP-3 dimer bound to myristoylated Arf1 (Q71L) and LAMP1 cargo on a lipid nanodisc
9C5B 4.5 Å, AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
9C58 4.7 Å, AP-3 bound to myristoylated Arf1 (Q71L)
9RTW 7.4 Å, Mammalian AP3 complex on tubular membranes (AP3 centered)

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