8JHC: FZD3 in inactive state

FZD3 in inactive state. Determined by electron microscopy at 3.3 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Escherichia coli, synthetic construct
Chains: 4
Atoms: 7,563
Mol. weight: 137.94 kDa
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8JHC contains 32 α-helices and 65 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 H: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	5
β-strand	14-15	2	6
β-strand	21-28	8	5
β-strand	36-42	7	7
β-strand	48-55	8	7
β-strand	62-63	2	7
β-strand	71-76	6	5
β-strand	81-86	6	5
α-helix	91-93	3
β-strand	95-102	8	7
α-helix	108-111	4
β-strand	117	1	7
β-strand	121-123	3	7
β-strand	124-125	2	6
β-strand	131	1	8
β-strand	134-137	4	9
α-helix	139-141	3
β-strand	149-159	11	9
β-strand	160	1	8
β-strand	165-168	4	10
β-strand	177-179	3	9
β-strand	183-184	2	9
β-strand	190-199	10	9
α-helix	203-205	3
β-strand	208-213	6	10
β-strand	214	1	11
β-strand	219	1	11
β-strand	222-225	4	10

Chain K: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	10-12	3	13
β-strand	19-25	7	12
β-strand	34-39	6	14
β-strand	46-51	6	14
β-strand	58-60	3	14
β-strand	69-73	5	12
β-strand	78-82	5	12
β-strand	93-99	7	14
β-strand	108-110	3	14
β-strand	115	1	14
β-strand	117-119	3	13

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	11-13	3	16
β-strand	20-26	7	15
β-strand	34-39	6	16
β-strand	46-50	5	16
β-strand	54-55	2	16
α-helix	56	1
β-strand	57	1	17
β-strand	59	1	17
β-strand	63-68	6	15
β-strand	71-76	6	15
β-strand	86-91	6	16
α-helix	95-97	3
β-strand	99-100	2	16
β-strand	104-107	4	16
α-helix	108-109	2
β-strand	118-120	3	18
α-helix	124-129	6
β-strand	131-139	9	18
β-strand	146-151	6	19
β-strand	156	1	19
β-strand	161-165	5	18
α-helix	166-169	4
β-strand	176-184	9	18
β-strand	193-200	8	19
α-helix	206	1
β-strand	207-212	6	19

Chain R: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	170	1	1
β-strand	178-179	2	2
β-strand	182-183	2	2
β-strand	185	1	1
β-strand	188	1	3
α-helix	196-226	31
α-helix	237-258	22
α-helix	265-267	3
β-strand	268	1	4
β-strand	273	1	4
β-strand	276	1	3
α-helix	286-313	28
α-helix	328-335	8
α-helix	338-348	11
α-helix	368-371	4
α-helix	372-376	5
α-helix	377-398	22
α-helix	1002-1023	22
α-helix	1030-1048	19
α-helix	1065-1085	21
α-helix	1089-1096	8
α-helix	1099-1106	8
α-helix	1110-1117	8
α-helix	413-444	32
α-helix	446-456	11
α-helix	464-466	3
α-helix	474-476	3
α-helix	477-486	10
α-helix	489-491	3
α-helix	493-498	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Frizzled-3,Soluble cytochrome b562	R	protein	643	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), Q9NPG1 (AlphaFold model)
anti-BRIL Fab Heavy chain	H	protein	240	Homo sapiens
anti-Fab Nanobody	K	protein	134	synthetic construct
anti-BRIL Fab Light chain	L	protein	212	Homo sapiens

Sequence of entity 1 (R), FASTA

>8JHC_1 Frizzled-3,Soluble cytochrome b562 (chains R)
MKTIIALSYIFCLVFADYKDDDDKHHHHHHHHHHENLYFQGHSLFSCEPITLRMCQDLPY
NTTFMPNLLNHYDQQTAALAMEPFHPMVNLDCSRDFRPFLCALYAPICMEYGRVTLPCRR
LCQRAYSECSKLMEMFGVPWPEDMECSRFPDCDEPYPRLVDLNLAGEPTEGAPVAVQRDY
GFWCPRELKIDPDLGYSFLHVRDCSPPCPNMYFRREELSFARYFIGLISIICLSATLFTF
LTFLIDVTRFRYPERPIIFYAVCYMMVSLIFFIGFLLEDRVACNASIPAQYKASTVTQGS
HNKACTMLFMILYFFTMAGSVWWVILTITWFLAAVPKWGSEAIEKKALLFHASAWGIPGT
LTIILLAMNKIEGDNISGVCFVGLYDVDALRYFVLAPLCLYVVVGVSLLLAGIISLNRRI
ARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDS
PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLNQ
DKLVKFMIRIGVFSILYLVPLLVVIGCYFYEQAYRGIWETTWIQERCREYHIPCPYQVTQ
MSRPDLILFLMKYLMALIVGIPSVFWVGSKKTCFEWASFFHGR

Sequence of entity 2 (H), FASTA

>8JHC_2 anti-BRIL Fab Heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGSTSY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSLEVLFQGPHHHHHH

Sequence of entity 3 (K), FASTA

>8JHC_3 anti-Fab Nanobody (chains K)
HHHHHHENLYFQGQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREF
VAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGS
YDYWGQGTQVTVSS

Sequence of entity 4 (L), FASTA

>8JHC_4 anti-BRIL Fab Light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Primary citation

A framework for Frizzled-G protein coupling and implications to the PCP signaling pathways. Zhang, Z., Lin, X., Wei, L. et al. Cell Discov (2024) 10:3-3. DOI 10.1038/s41421-023-00627-y · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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