6BD4: Human apo-Frizzled4 receptor

Crystal structure of human apo-Frizzled4 receptor. Determined by X-ray diffraction at 2.4 Å resolution. Released 22 Aug 2018.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Clostridium pasteurianum
Chains: 1
Atoms: 3,201
Mol. weight: 51.01 kDa
Ligands: OLA, OLC, ZN
Released: 22 Aug 2018

Explore 6BD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BD4 contains 22 α-helices and 14 β-strands across 1 chain. 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: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	194-195	2	1
β-strand	200-201	2	1
β-strand	203	1	2
α-helix	213-243	31
α-helix	245-247	3
α-helix	250-252	3
α-helix	253-275	23
α-helix	277-281	5
β-strand	282-283	2	2
β-strand	291-292	2	2
α-helix	300-327	28
α-helix	328-332	5
α-helix	337-341	5
α-helix	344-365	22
β-strand	368-370	3	3
β-strand	377-379	3	3
α-helix	384-387	4
α-helix	388-392	5
α-helix	393-417	25
α-helix	1001-1003	3
β-strand	1004-1006	3	4
β-strand	1012-1013	2	4
β-strand	1019	1	5
β-strand	1024	1	5
α-helix	1030-1032	3
β-strand	1038	1	6
β-strand	1045	1	6
α-helix	1046-1048	3
β-strand	1049-1051	3	4
α-helix	428-431	4
α-helix	432-443	12
α-helix	445-460	16
α-helix	462-467	6
α-helix	474-489	16
α-helix	492-495	4
α-helix	498-511	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Frizzled-4/Rubredoxin chimeric protein	A	protein	420	Homo sapiens, Clostridium pasteurianum	P00268 (AlphaFold model), Q9ULV1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6BD4_1 Frizzled-4/Rubredoxin chimeric protein (chains A)
DYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTLEGEECHSVGTNSDQYIWVKRSLNCVLK
CGYDAGLYSRSAKEFTDIWMAVWASLCFISTAFTVLTFLIDSSRFSYPERPIIFLSMCYN
IYSIAYIVRLTVGRERISCDFEEAAEPVLIQEGLKNTGCAIIFLLLYFFGMASSIWWVIL
TLTWFLAAGLKWGHEAIEMHSSYFHIAAWAIPAVKTIVILIMRLVDADELTGLCYVGNQN
LDALTGFVVAPLFTYLVIGTLFIAAGLVALFKIRSNMKKYTCTVCGYIYNPEDGDPDNGV
NPGTDFKDIPDDWVCPLCGVGKDQFEEVEEDKLERLMVKIGVFSVLYTVPATIVIACYFY
EISNWALFRYSADDSNMAVEMLKIFMSLLVGITSGMWIWSAKTLHTWQKFYNRLVNSGKV

Ligands and cofactors

ID	Name	Formula	Copies
OLA	Oleic acid	C18 H34 O2	5
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	4
ZN	Zinc ion	Zn	1

Water and common crystallization additives (UNX, SO4) are not listed.

Primary citation

Crystal structure of the Frizzled 4 receptor in a ligand-free state. Yang, S., Wu, Y., Xu, T.H. et al. Nature (2018) 560:666-670. DOI 10.1038/s41586-018-0447-x · PubMed

Other PDB entries of the same protein (UniProt P00268 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PVE 0.79 Å, NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of…
1IRO 1.1 Å, Rubredoxin (oxidized, fe(iii)) at 1.1 Å resolution
1IRN 1.2 Å, Rubredoxin (ZN-substituted) at 1.2 Å resolution
4RXN 1.2 Å, Crystallographic refinement of rubredoxin at 1.2 Å resolution
5RXN 1.2 Å, Combined crystallographic refinement and energy minimization of rubredoxin at 1.2 Å…
1SMM 1.36 Å, Crystal Structure of Cp Rd L41A mutant in oxidized state
1SMW 1.38 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 2 (soaked)
1SMU 1.43 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 1 (drop-reduced)
1B13 1.5 Å, Clostridium pasteurianum rubredoxin G10A mutant
1FHH 1.5 Å, X-ray crystal structure of oxidized rubredoxin
1FHM 1.5 Å, X-ray crystal structure of reduced rubredoxin
1R0I 1.5 Å, cadmium-substituted rubredoxin

Browse structure collections

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