3K48: APRIL

Crystal structure of APRIL bound to a peptide. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Nov 2009.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 6
Atoms: 3,613
Mol. weight: 53.21 kDa
Released: 24 Nov 2009

Explore 3K48 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3K48 contains 5 α-helices and 35 β-strands across 6 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: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	108-117	10	1
β-strand	125-135	11	1
β-strand	139-142	4	1
β-strand	145-148	4	1
β-strand	152-162	11	1
β-strand	168-176	9	1
β-strand	181-190	10	1
β-strand	200-210	11	1
β-strand	215-220	6	1
β-strand	227	1	1
β-strand	235-240	6	1

Chain B: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	108-117	10	2
β-strand	125-135	11	2
β-strand	139-142	4	2
β-strand	145-148	4	2
β-strand	152-162	11	2
β-strand	168-177	10	2
β-strand	180-190	11	2
β-strand	200-210	11	2
β-strand	215-220	6	2
β-strand	227	1	2
β-strand	235-240	6	2

Chain D: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	108-117	10	3
β-strand	125	1	4
β-strand	126-135	10	3
β-strand	139-142	4	5
β-strand	145-148	4	5
β-strand	152-162	11	3
β-strand	168-177	10	5
β-strand	180-190	11	5
β-strand	200-210	11	3
β-strand	215-219	5	5
β-strand	220	1	4
β-strand	227	1	3
β-strand	235-240	6	3

Chains R and S: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	11-13	3

Chain T: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor ligand superfamily member 13	A, B, D	protein	140	Mus musculus	Q9D777 (AlphaFold model)
peptide	R, S, T	protein	16

Sequence of entity 1 (A, B, D), FASTA

>3K48_1 Tumor necrosis factor ligand superfamily member 13 (chains A, B, D)
GSKKHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVL
FHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIP
RANAKLSLSPHGTFLGFVKL

Sequence of entity 2 (R, S, T), FASTA

>3K48_2 peptide (chains R, S, T)
SGWCDPRWYDPFMCEH

Primary citation

Multiple novel classes of APRIL-specific receptor-blocking peptides isolated by phage display. Gordon, N.C., Lien, S., Johnson, J. et al. J Mol Biol (2010) 396:166-177. DOI 10.1016/j.jmb.2009.11.041 · PubMed

Other PDB entries of the same protein (UniProt Q9D777 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U5X 1.8 Å, Crystal structure of murine APRIL at pH 5.0
1XU1 1.9 Å, The crystal structure of APRIL bound to TACI
1U5Y 2.3 Å, Crystal structure of murine APRIL, pH 8.0
1XU2 2.35 Å, The crystal structure of APRIL bound to BCMA
1U5Z 2.4 Å, The Crystal structure of murine APRIL, pH 8.5

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