PDB-6ne2: Designed repeat protein in complex with Fz7

ID or keywords:

Entry

Database: PDB / ID: 6ne2

Title

Designed repeat protein in complex with Fz7

Components

Designed repeat protein binder
Frizzled-7

Keywords

BIOSYNTHETIC PROTEIN/SIGNALING PROTEIN / Frizzled / Designed protein / BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN-SIGNALING PROTEIN complex

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

Biological species

Escherichia coli (E. coli)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.299 Å

Authors

Miao, Y. / Jude, K.M. / Garcia, K.C.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	1R01DK115728	United States
Howard Hughes Medical Institute (HHMI)		United States

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Receptor subtype discrimination using extensive shape complementary designed interfaces.
Authors: Dang, L.T. / Miao, Y. / Ha, A. / Yuki, K. / Park, K. / Janda, C.Y. / Jude, K.M. / Mohan, K. / Ha, N. / Vallon, M. / Yuan, J. / Vilches-Moure, J.G. / Kuo, C.J. / Garcia, K.C. / Baker, D.

History

Deposition	Dec 15, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 19, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ne2.cif.gz	151 KB	Display	PDBx/mmCIF format
PDB format	pdb6ne2.ent.gz	118.1 KB	Display	PDB format
PDBx/mmJSON format	6ne2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ne2_validation.pdf.gz	483.7 KB	Display	wwPDB validaton report
Full document	6ne2_full_validation.pdf.gz	484.5 KB	Display
Data in XML	6ne2_validation.xml.gz	16.6 KB	Display
Data in CIF	6ne2_validation.cif.gz	24.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ne/6ne2 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6ne2	HTTPS FTP

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Related structure data

Related structure data	6ndzC 6ne1C 6ne4C 5t44S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ndz-1 4dfb-1 4dtb-2 3ziv-d 4dt9-2 1xew-d 2fh4-2 6ndz-3 3bdx-d 4dtb-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #70 - Oct 2005 Designer Proteins similarity (1) #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)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (1)
#70 - Oct 2005
Designer Proteins
similarity (1)
#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

B: Designed repeat protein binder

A: Frizzled-7

hetero molecules

36.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.610, 68.040, 86.440
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-210- SO4

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Protein , 2 types, 2 molecules BA

#1: Protein	Designed repeat protein binder Mass: 20933.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein	Frizzled-7 / hFz7 / FzE3 Mass: 14111.210 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FZD7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75084

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Sugars , 1 types, 1 molecules

#6: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 289 molecules

#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.42 Å³/Da / Density % sol: 49.11 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Acetate: HCl, pH 4.5, 2 M Ammonium Sulfate

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.299→50 Å / Num. obs: 83592 / % possible obs: 99 % / Redundancy: 7 % / Net I/σ(I): 16.2
Reflection shell	Resolution: 1.299→1.35 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5T44

5t44

Resolution: 1.299→43.22 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.67

	R_factor	Num. reflection	% reflection
R_free	0.1843	4181	5 %
R_work	0.1615	-	-
obs	0.1627	83592	99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.299→43.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2331	0	108	268	2707

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2509
X-RAY DIFFRACTION	f_angle_d	0.968	3408
X-RAY DIFFRACTION	f_dihedral_angle_d	16.105	927
X-RAY DIFFRACTION	f_chiral_restr	0.078	382
X-RAY DIFFRACTION	f_plane_restr	0.006	450

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 (%)
1.2987-1.3134	0.3089	112	0.3122	2130	X-RAY DIFFRACTION	80
1.3134-1.3289	0.2635	130	0.2836	2469	X-RAY DIFFRACTION	94
1.3289-1.3451	0.2959	135	0.2773	2571	X-RAY DIFFRACTION	98
1.3451-1.3621	0.3093	138	0.256	2615	X-RAY DIFFRACTION	99
1.3621-1.3801	0.2429	140	0.2423	2653	X-RAY DIFFRACTION	100
1.3801-1.399	0.2431	138	0.2216	2620	X-RAY DIFFRACTION	100
1.399-1.419	0.2255	139	0.2112	2645	X-RAY DIFFRACTION	100
1.419-1.4401	0.239	141	0.1938	2677	X-RAY DIFFRACTION	100
1.4401-1.4626	0.2118	139	0.1835	2631	X-RAY DIFFRACTION	100
1.4626-1.4866	0.2073	139	0.1736	2655	X-RAY DIFFRACTION	100
1.4866-1.5123	0.1712	139	0.1668	2632	X-RAY DIFFRACTION	100
1.5123-1.5398	0.1977	138	0.1655	2627	X-RAY DIFFRACTION	100
1.5398-1.5694	0.1901	140	0.1638	2662	X-RAY DIFFRACTION	100
1.5694-1.6014	0.1885	141	0.1621	2662	X-RAY DIFFRACTION	100
1.6014-1.6362	0.178	139	0.1554	2639	X-RAY DIFFRACTION	100
1.6362-1.6743	0.1682	140	0.1628	2662	X-RAY DIFFRACTION	100
1.6743-1.7162	0.1735	139	0.1605	2651	X-RAY DIFFRACTION	100
1.7162-1.7626	0.1682	141	0.1599	2671	X-RAY DIFFRACTION	100
1.7626-1.8144	0.1873	140	0.1549	2652	X-RAY DIFFRACTION	100
1.8144-1.873	0.1867	140	0.163	2671	X-RAY DIFFRACTION	100
1.873-1.9399	0.1808	142	0.1596	2703	X-RAY DIFFRACTION	100
1.9399-2.0176	0.1837	140	0.158	2652	X-RAY DIFFRACTION	100
2.0176-2.1094	0.1824	142	0.1478	2684	X-RAY DIFFRACTION	100
2.1094-2.2206	0.1731	140	0.1534	2688	X-RAY DIFFRACTION	100
2.2206-2.3598	0.1831	141	0.1582	2679	X-RAY DIFFRACTION	100
2.3598-2.5419	0.2016	143	0.1518	2711	X-RAY DIFFRACTION	100
2.5419-2.7977	0.1902	143	0.1605	2710	X-RAY DIFFRACTION	100
2.7977-3.2024	0.1975	144	0.161	2739	X-RAY DIFFRACTION	100
3.2024-4.0343	0.1659	145	0.1425	2752	X-RAY DIFFRACTION	100
4.0343-43.2439	0.1532	153	0.1529	2898	X-RAY DIFFRACTION	100

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	0.7981	0.4446	0.7517	1.2038	0.9267	1.1549	0.0285	-0.1318	-0.1191	0.151	0.0054	-0.2463	0.1411	0.1356	-0.0115	0.1644	0.0043	-0.0198	0.159	-0.0059	0.1626	-93.474	-335.8562	190.528
2	1.2334	-0.1848	0.5492	0.9549	-0.4458	1.6499	0.0095	-0.0132	0.0202	-0.0374	0.0725	0.0608	0.008	-0.223	-0.0767	0.1092	-0.0004	0.0051	0.1483	0.0027	0.1239	-108.7178	-327.0672	179.5324
3	1.6258	-0.2599	-0.3871	1.5392	-0.4966	2.4554	0.0217	0.2413	-0.0801	-0.2318	0.0651	0.0885	0.0921	-0.1226	-0.0825	0.1872	-0.0051	-0.0371	0.267	0.0207	0.1851	-119.7001	-325.1582	158.2829
4	3.9679	-1.6529	-0.05	2.5895	-0.5311	2.2905	-0.097	-0.0863	-0.0401	0.0322	-0.0027	-0.1494	-0.0364	0.079	0.0408	0.1286	-0.0174	-0.0052	0.1227	0.0007	0.1558	-87.9949	-336.1033	167.1213
5	2.916	-0.2658	0.2321	1.8429	-1.3106	1.6776	0.0358	0.2513	-0.0296	-0.1006	0.0047	-0.1195	0.0125	0.1893	-0.0132	0.1454	-0.0022	0.0056	0.1328	0.0005	0.1682	-85.6388	-332.8645	166.5473
6	1.0106	-0.4246	-0.2628	0.9442	-0.3219	0.867	0.0591	0.1042	0.003	-0.1281	-0.0164	0.05	-0.0492	-0.1073	-0.1004	0.1573	0.0092	-0.0055	0.1435	0.0058	0.1402	-96.9965	-325.1154	169.4398
7	1.4674	-0.346	-0.4139	1.3084	-0.6098	1.6008	0.1179	0.0167	0.0325	-0.0358	-0.0462	-0.1796	-0.3328	0.0541	-0.0292	0.1512	-0.0049	0.0107	0.1148	0.002	0.1547	-89.8526	-324.2298	165.9855
8	0.993	0.8076	-0.9461	2.349	0.0945	2.3958	-0.1016	-0.0497	-0.0631	-0.1179	0.0179	-0.4839	-0.0265	0.2448	0.0012	0.1158	-0.0102	0.0164	0.1614	0.0149	0.2147	-78.0449	-328.6348	165.1293
9	2.0722	-0.5545	-0.9219	0.4848	0.3485	1.4165	0.3954	0.1033	0.5695	0.1745	-0.0325	0.0911	-0.4016	-0.0315	-0.1149	0.2641	0.0238	0.1117	0.116	0.0206	0.2393	-92.6201	-312.2663	165.8198
10	4.0334	-0.3356	-1.1666	0.0619	-0.1215	2.3151	0.1674	-0.4457	0.3497	0.3284	-0.0114	0.1813	-0.2811	0.4176	-0.1504	0.3413	-0.0828	0.1445	0.1543	-0.0766	0.2517	-90.6138	-313.445	173.8404
11	1.1883	0.2062	-0.8234	1.5434	0.2068	1.5482	0.0868	0.2138	-0.0518	-0.0641	-0.0249	-0.097	0.0686	0.009	-0.0296	0.2006	-0.0227	0.027	0.1752	0.0148	0.1991	-78.51	-318.8949	160.526

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid -1 through 24 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 25 through 137 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 138 through 191 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 2 through 12 )
5	X-RAY DIFFRACTION	5	chain 'A' and ((resid 13 through 30) or resid 121)
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 31 through 52 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 53 through 61 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 62 through 75 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 76 through 92 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 93 through 105 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 106 through 120 )

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