8WM9: Fzd4/DEP complex

Fzd4/DEP complex. Determined by electron microscopy at 3.53 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.53 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,879
Mol. weight: 204 kDa
Ligands: Y01
Released: 11 Sept 2024

Explore 8WM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WM9 contains 35 α-helices and 16 β-strands across 3 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: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	191-193	3	1
β-strand	200-202	3	1
β-strand	203	1	2
α-helix	204	1
α-helix	213-243	31
α-helix	253-275	23
α-helix	277-280	4
β-strand	291	1	2
α-helix	296-298	3
α-helix	300-331	32
α-helix	341-343	3
α-helix	344-365	22
β-strand	369-370	2	3
β-strand	377-378	2	3
α-helix	384-386	3
α-helix	387-392	6
α-helix	393-420	28
α-helix	428-460	33
α-helix	462-464	3
α-helix	472-489	18
α-helix	493-495	3
α-helix	498-510	13

Chain B: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	213-243	31
α-helix	245-247	3
α-helix	254-275	22
α-helix	277-280	4
β-strand	282	1	4
β-strand	292	1	4
α-helix	300-306	7
α-helix	307-311	5
α-helix	312-331	20
α-helix	337-341	5
α-helix	344-365	22
β-strand	368-370	3	5
β-strand	377-379	3	5
α-helix	384-387	4
α-helix	388-392	5
α-helix	393-417	25
α-helix	433-460	28
α-helix	462-467	6
α-helix	472-489	18
α-helix	498-512	15

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	423-430	8
β-strand	440-444	5	6
β-strand	447-452	6	6
β-strand	453-454	2	7
α-helix	455-464	10
α-helix	475-484	10
β-strand	489	1	8
β-strand	502-503	2	7
β-strand	504	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Frizzled-4	A, B	protein	537	Homo sapiens	Q9ULV1 (AlphaFold model)
Segment polarity protein dishevelled homolog DVL-2	C	protein	736	Homo sapiens	O14641 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8WM9_1 Frizzled-4 (chains A, B)
MAWRGAGPSVPGAPGGVGLSLGLLLQLLLLLGPARGFGDEEERRCDPIRISMCQNLGYNV
TKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGM
CLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEGPGDEEVPLPHKTPIQPGEE
CHSVGTNSDQYIWVKRSLNCVLKCGYDAGLYSRSAKEFTDIWMAVWASLCFISTAFTVLT
FLIDSSRFSYPERPIIFLSMCYNIYSIAYIVRLTVGRERISCDFEEAAEPVLIQEGLKNT
GCAIIFLLLYFFGMASSIWWVILTLTWFLAAGLKWGHEAIEMHSSYFHIAAWAIPAVKTI
VILIMRLVDADELTGLCYVGNQNLDALTGFVVAPLFTYLVIGTLFIAAGLVALFKIRSNL
QKDGTKTDKLERLMVKIGVFSVLYTVPATIVIACYFYEISNWALFRYSADDSNMAVEMLK
IFMSLLVGITSGMWIWSAKTLHTWQKFYNRLVNSGKVKREKRGNGWVKPGKGSETVV

Sequence of entity 2 (C), FASTA

>8WM9_2 Segment polarity protein dishevelled homolog DVL-2 (chains C)
MAGSSTGGGGVGETKVIYHLDEEETPYLVKIPVPAERITLGDFKSVLQRPAGAKYFFKSM
DQDFGVVKEEISDDNARLPCFNGRVVSWLVSSDNPQPEMAPPVHEPRAELAPPAPPLPPL
PPERTSGIGDSRPPSFHPNVSSSHENLEPETETESVVSLRRERPRRRDSSEHGAGGHRTG
GPSRLERHLAGYESSSTLMTSELESTSLGDSDEEDTMSRFSSSTEQSSASRLLKRHRRRR
KQRPPRLERTSSFSSVTDSTMSLNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIM
KGGAVAADGRIEPGDMLLQVNDMNFENMSNDDAVRVLRDIVHKPGPIVLTVAKCWDPSPQ
AYFTLPRNEPIQPIDPAAWVSHSAALTGTFPAYPGSSSMSTITSGSSLPDGCEGRGLSVH
TDMASVTKAMAAPESGLEVRDRMWLKITIPNAFLGSDVVDWLYHHVEGFPERREARKYAS
GLLKAGLIRHTVNKITFSEQCYYVFGDLSGGCESYLVNLSLNDNDGSSGASDQDTLAPLP
GATPWPLLPTFSYQYPAPHPYSPQPPPYHELSSYTYGGGSASSQHSEGSRSSGSTRSDGG
AGRTGRPEERAPESKSGSGSESEPSSRGGSLRRGGEASGTSDGGPPPSRGSTGGAPNLRA
HPGLHPYGPPPGMALPYNPMMVVMMPPPPPPVPPAVQPPGAPPVRDLGSVPPELTASRQS
FHMAMGNPSEFFVDVM

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	10

Primary citation

Structural basis of Frizzled 4 in recognition of Dishevelled 2 unveils mechanism of WNT signaling activation. Qian, Y., Ma, Z., Xu, Z. et al. Nat Commun (2024) 15:7644-7644. DOI 10.1038/s41467-024-52174-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…
6NE1 3.01 Å, Designed repeat protein in complex with Fz4
8WMA 3.47 Å, Fzd4/DEP complex (local refined)
5CL1 3.8 Å, Complex structure of Norrin with human Frizzled 4

Browse structure collections

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