6NE1: Designed repeat protein

Designed repeat protein in complex with Fz4. Determined by X-ray diffraction at 3.01 Å resolution. Released 15 May 2019.

Method: X-ray diffraction
Resolution: 3.01 Å
Organisms: Homo sapiens, Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
Chains: 2
Atoms: 2,062
Mol. weight: 34.01 kDa
Ligands: NAG
Released: 15 May 2019

Explore 6NE1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NE1 contains 20 α-helices and 6 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	1
α-helix	51-53	3
β-strand	60-61	2	1
α-helix	72-79	8
α-helix	80-82	3
α-helix	83-88	6
α-helix	94-102	9
β-strand	105-106	2	1
β-strand	113-114	2	1
β-strand	116	1	2
α-helix	118-133	16
α-helix	141-143	3
β-strand	159	1	2

Chain B: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	3-13	11
α-helix	16-23	8
α-helix	39-46	8
α-helix	49-57	9
α-helix	67-69	3
α-helix	72-78	7
α-helix	82-91	10
α-helix	100-102	3
α-helix	105-111	7
α-helix	115-123	9
α-helix	133-135	3
α-helix	138-144	7
α-helix	148-155	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Frizzled-4	A	protein	120	Homo sapiens	Q9ULV1 (AlphaFold model)
Pfs, NACHT and Ankyrin domain protein	B	protein	192	Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)

Sequence of entity 1 (A), FASTA

>6NE1_1 Frizzled-4 (chains A)
ERRCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSV
YVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEG

Sequence of entity 2 (B), FASTA

>6NE1_2 Pfs, NACHT and Ankyrin domain protein (chains B)
SELGKRLIRAALDGNKDRVKDLIENGADVNASLMSGTTPLYAAAMNGHKEVVKLLISKGA
DVNAQSVAGSTPLVAAANFGHNEVVKLLISKGADVNAVTAFGVTPLHAAAADGHKEVVKL
LISKGADVNAKAGRGMTPLHIAAFRGHKEVVKLLISKGADLNTSAKDGATPLDMARESGN
EEVVKLLEKQLE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Receptor subtype discrimination using extensive shape complementary designed interfaces. Dang, L.T., Miao, Y., Ha, A. et al. Nat Struct Mol Biol (2019) 26:407-414. DOI 10.1038/s41594-019-0224-z · PubMed

Other PDB entries of the same protein (UniProt Q9ULV1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BPB 2.2 Å, Crystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form I
5BQE 2.3 Å, Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4…
5BPQ 2.4 Å, Crystal structure of the cysteine-rich domain of human Frizzled 4 - Crystal Form II
5CM4 2.4 Å, Crystal structure of human Frizzled 4 Cysteine-Rich Domain (CRD)
6BD4 2.4 Å, Crystal structure of human apo-Frizzled4 receptor
5UWG 2.56 Å, The crystal structure of Fz4-CRD in complex with palmitoleic acid
5BQC 3.0 Å, Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and…
8WMA 3.47 Å, Fzd4/DEP complex (local refined)
8WM9 3.53 Å, Fzd4/DEP complex
5CL1 3.8 Å, Complex structure of Norrin with human Frizzled 4

Browse structure collections

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