PDB-5wbs: Crystal structure of Frizzled-7 CRD with an inhibitor peptide Fz7-21

ID or keywords:

Entry

Database: PDB / ID: 5wbs

Title

Crystal structure of Frizzled-7 CRD with an inhibitor peptide Fz7-21

Components

Frizzled-7,inhibitor peptide Fz7-21

Keywords

SIGNALING PROTEIN /

Frizzled /

Wnt signaling /

inhibitor /

dimerization

Function / homology

Function and homology information

negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration /

Wnt receptor activity / somatic stem cell division / non-canonical Wnt signaling pathway / Wnt-protein binding / positive regulation of epithelial cell proliferation involved in wound healing / WNT5:FZD7-mediated leishmania damping ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.88 Å

Authors

Nile, A.H. / Mukund, S. / Hannoush, R.N. / Wang, W.

Citation

Journal: Nat. Chem. Biol. / Year: 2018
Title: A selective peptide inhibitor of Frizzled 7 receptors disrupts intestinal stem cells.
Authors: Nile, A.H. / de Sousa E Melo, F. / Mukund, S. / Piskol, R. / Hansen, S. / Zhou, L. / Zhang, Y. / Fu, Y. / Gogol, E.B. / Komuves, L.G. / Modrusan, Z. / Angers, S. / Franke, Y. / Koth, C. / ...

History

Deposition	Jun 29, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 25, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	May 30, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5wbs.cif.gz	425.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5wbs.ent.gz	365.3 KB	Display	PDB format
PDBx/mmJSON format	5wbs.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/5wbs ftp://data.pdbj.org/pub/pdb/validation_reports/wb/5wbs	HTTPS FTP

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Related structure data

Related structure data	5w96C C: citing same article (ref.)
Similar structure data	1oxq-7 2f1r-d 3kp9-d 1oxn-7 5he8-1 4m6d-1 4nv5-2 4nv6-d 3l9j-d 3ckg-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5w96C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (2) #184 - Apr 2015 Glucagon similarity (2) #122 - Feb 2010 Enhanceosome similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Frizzled-7,inhibitor peptide Fz7-21

B: Frizzled-7,inhibitor peptide Fz7-21

C: Frizzled-7,inhibitor peptide Fz7-21

D: Frizzled-7,inhibitor peptide Fz7-21

E: Frizzled-7,inhibitor peptide Fz7-21

F: Frizzled-7,inhibitor peptide Fz7-21

G: Frizzled-7,inhibitor peptide Fz7-21

H: Frizzled-7,inhibitor peptide Fz7-21

161 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Frizzled-7,inhibitor peptide Fz7-21

B: Frizzled-7,inhibitor peptide Fz7-21

defined by author&software
Evidence: gel filtration
40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Frizzled-7,inhibitor peptide Fz7-21

D: Frizzled-7,inhibitor peptide Fz7-21

defined by author&software
40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Frizzled-7,inhibitor peptide Fz7-21

F: Frizzled-7,inhibitor peptide Fz7-21

defined by author&software
40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Frizzled-7,inhibitor peptide Fz7-21

H: Frizzled-7,inhibitor peptide Fz7-21

defined by author&software
40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.610, 164.650, 97.770
Angle α, β, γ (deg.)	90.00, 108.31, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Frizzled-7,inhibitor peptide Fz7-21 / hFz7 / FzE3 Mass: 20105.289 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FZD7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75084
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 58.65 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1-propanol 14% (v/v; cat. no. 09158; Fluka), 9% PEG5000 MME (cat. no. HR-2-615; Hampton Research), and 0.1 M MES at pH 6.9 (cat. no. HR2-243; Hampton Research)

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.88→50 Å / Num. obs: 42391 / Redundancy: 3 % / Net I/σ(I): 7.4

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.88→38.717 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.39 / Phase error: 26.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2443	3831	5.02 %
R_work	0.1991	-	-
obs	0.2013	76382	91.11 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.88→38.717 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8359	0	0	1	8360

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8633
X-RAY DIFFRACTION	f_angle_d	1.045	11673
X-RAY DIFFRACTION	f_dihedral_angle_d	14.647	3139
X-RAY DIFFRACTION	f_chiral_restr	0.039	1237
X-RAY DIFFRACTION	f_plane_restr	0.005	1549

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.88-2.9164	0.3737	138	0.3607	2563	X-RAY DIFFRACTION	89
2.9164-2.9548	0.3295	155	0.3526	2620	X-RAY DIFFRACTION	88
2.9548-2.9953	0.3148	129	0.3133	2605	X-RAY DIFFRACTION	87
2.9953-3.038	0.3151	148	0.3048	2563	X-RAY DIFFRACTION	89
3.038-3.0834	0.3576	158	0.3016	2607	X-RAY DIFFRACTION	88
3.0834-3.1315	0.3417	123	0.2788	2647	X-RAY DIFFRACTION	89
3.1315-3.1828	0.3545	145	0.279	2710	X-RAY DIFFRACTION	92
3.1828-3.2377	0.3108	134	0.275	2701	X-RAY DIFFRACTION	92
3.2377-3.2965	0.3305	162	0.2676	2760	X-RAY DIFFRACTION	92
3.2965-3.3599	0.3791	143	0.2648	2646	X-RAY DIFFRACTION	91
3.3599-3.4285	0.2777	156	0.2634	2644	X-RAY DIFFRACTION	91
3.4285-3.503	0.3163	166	0.2463	2732	X-RAY DIFFRACTION	91
3.503-3.5844	0.2688	138	0.2449	2554	X-RAY DIFFRACTION	89
3.5844-3.674	0.2657	102	0.2394	2674	X-RAY DIFFRACTION	88
3.674-3.7732	0.2616	144	0.2163	2670	X-RAY DIFFRACTION	90
3.7732-3.8841	0.2568	128	0.214	2641	X-RAY DIFFRACTION	90
3.8841-4.0094	0.2741	174	0.1907	2685	X-RAY DIFFRACTION	93
4.0094-4.1525	0.2385	125	0.1761	2800	X-RAY DIFFRACTION	93
4.1525-4.3186	0.2199	130	0.1634	2706	X-RAY DIFFRACTION	92
4.3186-4.5149	0.1954	127	0.1537	2766	X-RAY DIFFRACTION	93
4.5149-4.7525	0.201	120	0.1467	2685	X-RAY DIFFRACTION	91
4.7525-5.0497	0.1964	151	0.1534	2718	X-RAY DIFFRACTION	92
5.0497-5.4386	0.2045	168	0.1561	2775	X-RAY DIFFRACTION	94
5.4386-5.9841	0.1813	119	0.162	2799	X-RAY DIFFRACTION	95
5.9841-6.8459	0.2607	163	0.1798	2738	X-RAY DIFFRACTION	93
6.8459-8.6094	0.2254	136	0.1694	2729	X-RAY DIFFRACTION	93
8.6094-38.7208	0.1999	149	0.1932	2813	X-RAY DIFFRACTION	95

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.571	-0.1666	-0.5005	0.1201	0.0942	0.5586	0.0535	0.1427	-0.1621	0.0157	-0.1259	0.0137	-0.0782	0.2033	-0.0002	0.3768	-0.0082	-0.0407	0.4604	0.0258	0.4648	23.3799	30.9179	22.6269
2	0.9415	-0.0682	0.2915	0.5495	-0.8116	0.9416	0.2327	0.1404	-0.0107	0.1776	-0.1285	0.1869	-0.1797	0.101	0.0002	0.6401	0.0019	0.1112	0.3561	0.0426	0.4931	4.4177	15.9355	49.5161
3	0.4475	0.5952	0.1638	0.5657	0.3558	0.7038	-0.1663	0.0162	0.226	0.0754	-0.202	0.5081	0.1483	0.0468	-0.0167	0.4643	-0.0678	-0.0744	0.3394	-0.0174	0.536	12.7581	57.0377	34.7759
4	0.4081	-0.3112	0.3575	0.4845	-0.4234	0.2995	-0.377	-0.2531	0.1886	0.2947	-0.1069	-0.0482	0.0561	0.2162	-0.0031	0.7806	0.001	-0.0813	0.6784	0.0299	0.5586	39.4894	71.2339	53.5736
5	0.2227	0.0716	0.2536	0.1672	0.2728	0.5265	-0.3077	0.1614	-0.302	-0.0944	-0.1459	0.3581	-0.2466	0.1261	-0.1229	0.4466	0.0981	0.165	0.5866	-0.0754	0.6076	-18.7135	17.4906	-4.6254
6	0.6101	-0.506	-0.1237	0.3124	0.0436	0.3877	-0.3139	-0.242	-0.5121	0.1866	-0.0206	0.3322	-0.0139	-0.0689	0.0002	0.6113	0.0107	0.1479	0.7075	-0.1692	0.6572	8.6594	2.6538	-23.0305
7	0.7876	0.0542	0.5107	0.5235	0.5478	0.7902	0.0428	0.0645	0.085	0.012	-0.1506	0.002	0.0142	0.1399	-0	0.3813	0.0021	0.0035	0.5637	0.0563	0.4571	-8.0351	43.6853	7.7804
8	0.4741	0.2091	0.0374	0.6282	-0.5962	0.5642	-0.1265	-0.0319	-0.1413	-0.1319	0.1107	0.1924	-0.051	0.0789	-0.0001	0.8314	-0.0381	-0.1959	0.8076	0.2909	0.6022	-27.2049	58.8921	-18.7993

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H

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