7EAA: NDP52 SKICH domain

crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain. Determined by X-ray diffraction at 2.6 Å resolution. Released 22 Dec 2021.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,757
Mol. weight: 59.07 kDa
Released: 22 Dec 2021

Explore 7EAA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EAA contains 11 α-helices and 22 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: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	4
β-strand	31-32	2	5
β-strand	38-44	7	4
β-strand	55-60	6	6
α-helix	66-68	3
β-strand	69-74	6	6
α-helix	75-77	3
β-strand	89-93	5	4
α-helix	95-97	3
β-strand	105-110	6	6
β-strand	116-119	4	6
β-strand	123	1	6
β-strand	124-125	2	5

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	15-17	3
β-strand	18	1	1
β-strand	21	1	1
β-strand	23-24	2	2
β-strand	31	1	3
β-strand	38-44	7	2
β-strand	55-60	6	1
α-helix	66-68	3
β-strand	72-74	3	1
β-strand	88-93	6	2
α-helix	95-97	3
β-strand	105-110	6	1
β-strand	116-119	4	1
α-helix	120-122	3
β-strand	123	1	1
β-strand	124	1	3

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1284-1393	110

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1287-1341	55
α-helix	1344-1393	50

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RB1-inducible coiled-coil protein 1	C, D	protein	114	Homo sapiens	Q8TDY2 (AlphaFold model)
Calcium-binding and coiled-coil domain-containing protein 2	A, B	protein	136	Homo sapiens	Q13137 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>7EAA_1 RB1-inducible coiled-coil protein 1 (chains C, D)
GSEFSLVAELQEKLQEEKAKFLEQLEEQEKRKNEEMQNVRTSLIAEQQTNFNTVLTREKM
RKENIINDLSDKLKSTMQQQERDKDLIESLSEDRARLLEEKKKLEEEVSKLRSS

Sequence of entity 2 (A, B), FASTA

>7EAA_2 Calcium-binding and coiled-coil domain-containing protein 2 (chains A, B)
GPGSTSAVLLDHCHFSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKT
TREYYTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQF
RPENEEDILVVTTQGE

Primary citation

Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52. Fu, T., Zhang, M., Zhou, Z. et al. Sci Adv (2021) 7. DOI 10.1126/sciadv.abi6582 · PubMed

Other PDB entries of the same protein (UniProt Q8TDY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7D0E 1.4 Å, Crystal structure of FIP200 Claw/p-CCPG1 FIR2
9D34 1.42 Å, FIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with phosphorylated TNIP1…
8YFL 1.5 Å, crystal structure of FIP200 claw/TNIP1_FIR_pS122pS123
8YFM 1.5 Å, Crystal structure of FIP200 claw/TNIP1_FIR_pS122
6DCE 1.56 Å, X-ray structure of FIP200 claw domain
9J54 1.61 Å, Crystal structure of FIP200 Claw in complex with ATG16L1
7CZG 1.8 Å, Crystal structure of FIP200 Claw domain apo form
9LUA 1.97 Å, Crystal structure of FIP200 Claw domain and SMCR8 FIR motif complex
7CZM 2.0 Å, Crystal structure of FIP200 Claw/p-OPtineurin LIR complex
8YFK 2.0 Å, Crystal structure of FIP200 claw/TNIP1_FIR_pS123
7EA2 2.14 Å, crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain
8YFN 2.3 Å, Crystal structure of FIP200 claw in complex with TNIP1_FIR_pS123 peptide with an…

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