5BQE: Norrin

Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 -Methylated form. Determined by X-ray diffraction at 2.3 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,711
Mol. weight: 44.71 kDa
Ligands: NAG, PG0
Released: 1 Jul 2015

Explore 5BQE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BQE contains 12 α-helices and 28 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: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	40-48	9	1
β-strand	55	1	2
β-strand	58-67	10	1
α-helix	72	1
β-strand	73-77	5	3
β-strand	80	1	4
β-strand	89-92	4	3
β-strand	94-109	16	5
β-strand	110	1	2
β-strand	115-130	16	5

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	38	1	6
β-strand	40-48	9	3
β-strand	58-67	10	3
β-strand	68	1	6
α-helix	72	1
β-strand	73-77	5	1
β-strand	80	1	5
β-strand	81	1	7
β-strand	84	1	7
β-strand	89-92	4	1
β-strand	94-107	14	4
β-strand	117-130	14	4

Chain C: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	8
α-helix	48	1
α-helix	51-53	3
β-strand	60-61	2	8
α-helix	72-79	8
α-helix	80-82	3
α-helix	83-87	5
α-helix	94-102	9
β-strand	105	1	8
β-strand	114	1	8
β-strand	115-116	2	9
α-helix	118-134	17
α-helix	138-140	3
α-helix	141-143	3
α-helix	145-147	3
β-strand	153	1	10
β-strand	156	1	10
β-strand	158-159	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Norrin	A	protein	122	Homo sapiens	Q00604 (AlphaFold model)
Norrin	B	protein	122	Homo sapiens	Q00604 (AlphaFold model)
Frizzled-4	C	protein	149	Homo sapiens	Q9ULV1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5BQE_1 Norrin (chains A)
GPGKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSF
STVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNSGTETSQVA
PA

Sequence of entity 2 (B), FASTA

>5BQE_2 Norrin (chains B)
GPGKTDSSFIMDSDPRRCMRHHYVDSISHPLYKCSSKMVLLARCEGHCSQASRSEPLVSF
STVLKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLTATYRYILSCHCEECNSGTETSQVA
PA

Sequence of entity 3 (C), FASTA

>5BQE_3 Frizzled-4 (chains C)
DTGERRCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFL
CSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMC
MEGPGDEEVPLPHKTPIQPGEGTLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PG0	2-(2-methoxyethoxy)ethanol	C5 H12 O3	3

Water and common crystallization additives (CL) are not listed.

Primary citation

Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan. Chang, T.H., Hsieh, F.L., Zebisch, M. et al. Elife (2015) 4:e06554. DOI 10.7554/eLife.06554 · PubMed

Other PDB entries of the same protein (UniProt Q00604 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BQ8 2.0 Å, Crystal structure of Norrin, a Wnt signalling activator, Crystal Form II
5BQB 2.3 Å, Crystal structure of Norrin, a Wnt signalling activator, Crystal Form III
5BPU 2.4 Å, Crystal structure of Norrin, a Wnt signalling activator, Crystal Form I
5BQC 3.0 Å, Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and…
9UOK 3.05 Å, Structure of the complex of LGR4_ECD with Norrin
8WVY 3.29 Å, Cryo-EM structure of LGR4 in complex with Norrin
8WVX 3.32 Å, Cryo-EM structure of LGR4 in complex with Norrin(dimer)
9KHH 3.65 Å, Structure of the complex of LGR4 with Norrin (2:2)
9MAN 3.78 Å, Structure of Norrin in complex with human Tspan12 large extracellular loop (Tspan12 LEL)
5CL1 3.8 Å, Complex structure of Norrin with human Frizzled 4

Browse structure collections

About this viewer

MolViewer shows 5BQE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.