5DPR: PLEKHM1 LIR-fused human LC3A_2-121

Crystal structure of PLEKHM1 LIR-fused human LC3A_2-121. Determined by X-ray diffraction at 2.5 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,128
Mol. weight: 63.73 kDa
Released: 28 Sept 2016

Explore 5DPR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DPR contains 25 α-helices and 28 β-strands across 4 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	24-37	14
β-strand	41-48	8	1
α-helix	56-58	3
β-strand	62-66	5	1
β-strand	70	1	2
α-helix	71-81	11
β-strand	91-93	3	1
β-strand	98	1	1
β-strand	105	1	2
α-helix	106-113	8
α-helix	119	1
β-strand	120-125	6	1

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	24-37	14
β-strand	41-48	8	3
α-helix	56-58	3
β-strand	62-66	5	3
β-strand	70	1	4
α-helix	71-81	11
β-strand	91-94	4	3
β-strand	97	1	3
β-strand	105	1	4
α-helix	106-113	8
α-helix	119	1
β-strand	120-125	6	3

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	24-37	14
β-strand	41-48	8	5
α-helix	56-58	3
β-strand	62-66	5	5
β-strand	70	1	6
α-helix	71-82	12
β-strand	91-94	4	5
β-strand	97	1	5
β-strand	105	1	6
α-helix	106-113	8
α-helix	119	1
β-strand	120-125	6	5

Chain D: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	24-37	14
β-strand	41-48	8	7
α-helix	56-58	3
β-strand	62-66	5	7
β-strand	70	1	8
α-helix	71-81	11
β-strand	91-93	3	7
β-strand	98	1	7
α-helix	99-101	3
β-strand	105	1	8
α-helix	106-113	8
α-helix	119	1
β-strand	120-125	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B…	A, B, C, D	protein	136	Homo sapiens	Q9H492 (AlphaFold model), Q9Y4G2 (AlphaFold model)

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

>5DPR_1 Pleckstrin homology domain-containing family M member 1,Microtubule-associated proteins 1A/1B light chain 3A (chains A, B, C, D)
GSVRPQQEDEWVNVGSPSDRPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLP
VLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDE
DGFLYMVYASQETFGF

Primary citation

Structural and functional analysis of the GABARAP interaction motif (GIM). Rogov, V.V., Stolz, A., Ravichandran, A.C. et al. EMBO Rep (2017) 18:1382-1396. DOI 10.15252/embr.201643587 · PubMed

Other PDB entries of the same protein (UniProt Q9H492 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RA0 1.36 Å, LC3A in complex with Fragment 2-10
6TBE 1.67 Å, LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzam…
7R9Z 1.72 Å, LC3A in complex with Fragment 2-3
7R9W 1.75 Å, LC3A in complex with Fragment 1-1
3WAN 1.77 Å, Crystal structure of Atg13 LIR-fused human LC3A_2-121
4ZDV 1.8 Å, Crystal structure of LC3 in complex with FAM134B LIR
8T36 1.85 Å, Crystal structure of K49 acetylated LC3A in complex with the LIR of TP53INP2/DOR
8T35 1.9 Å, Crystal structure of K51 acetylated LC3A in complex with the LIR of TP53INP2/DOR
3WAL 2.0 Å, Crystal structure of human LC3A_2-121
8T2L 2.24 Å, Crystal structure of LC3A in complex with the LIR of NSs4
5CX3 2.3 Å, Crystal structure of FYCO1 LIR in complex with LC3A
8T4T 2.36 Å, Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR

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