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- PDB-6tfm: Frizzled8 CRD -

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Basic information

Entry
Database: PDB / ID: 6tfm
TitleFrizzled8 CRD
ComponentsFrizzled-8
KeywordsONCOPROTEIN / Wnt receptor Frizzled8 CRD
Function / homology
Function and homology information


Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / Wnt-protein binding / neuronal dense core vesicle / canonical Wnt signaling pathway / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway ...Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / Wnt-protein binding / neuronal dense core vesicle / canonical Wnt signaling pathway / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway / T cell differentiation in thymus / angiogenesis / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / extracellular region / plasma membrane
Similarity search - Function
Frizzled 8, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. ...Frizzled 8, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.343 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M000141/1 United Kingdom
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: Antiepileptic Drug Carbamazepine Binds to a Novel Pocket on the Wnt Receptor Frizzled-8.
Authors: Zhao, Y. / Ren, J. / Hillier, J. / Lu, W. / Jones, E.Y.
History
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Frizzled-8
D: Frizzled-8
B: Frizzled-8
C: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)63,2604
Polymers63,2604
Non-polymers00
Water88349
1
A: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Frizzled-8


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.296, 66.039, 72.666
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 34 through 153 or resid 156 through 162))
21(chain B and (resid 34 through 153 or resid 156 through 162))
31(chain C and resid 34 through 162)
41chain D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARG(chain A and (resid 34 through 153 or resid 156 through 162))AA34 - 15310 - 129
12LEULEUGLYGLY(chain A and (resid 34 through 153 or resid 156 through 162))AA156 - 162132 - 138
21ALAALAARGARG(chain B and (resid 34 through 153 or resid 156 through 162))BC34 - 15310 - 129
22LEULEUGLYGLY(chain B and (resid 34 through 153 or resid 156 through 162))BC156 - 162132 - 138
31ALAALAGLYGLY(chain C and resid 34 through 162)CD34 - 16210 - 138
41ALAALAGLYGLYchain DDB34 - 16210 - 138

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Components

#1: Protein
Frizzled-8 / mFz8


Mass: 15815.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fzd8 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q61091
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium acetate, pH 5 1 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.34→72.7 Å / Num. obs: 20741 / % possible obs: 98.9 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.3
Reflection shellResolution: 2.34→2.38 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1024 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIXdev_3488refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJY

1ijy


Resolution: 2.343→72.666 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.75
RfactorNum. reflection% reflection
Rfree0.3004 1012 5.15 %
Rwork0.2432 --
obs0.246 19646 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.67 Å2 / Biso mean: 20.6271 Å2 / Biso min: 3.27 Å2
Refinement stepCycle: final / Resolution: 2.343→72.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 0 49 4199
Biso mean---12.94 -
Num. residues----513
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2532X-RAY DIFFRACTION15.108TORSIONAL
12B2532X-RAY DIFFRACTION15.108TORSIONAL
13C2532X-RAY DIFFRACTION15.108TORSIONAL
14D2532X-RAY DIFFRACTION15.108TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.343-2.46650.31651470.2842222780
2.4665-2.62110.36941280.2667243286
2.6211-2.82350.33851300.2698262593
2.8235-3.10760.31271700.2613279799
3.1076-3.55730.27981520.2452280999
3.5573-4.48170.25491470.2181284099
4.4817-72.660.30031380.2149290499
Refinement TLS params.

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

IDL11 (°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)
10.0044-0.0327-0.00490.25080.0360.00530.0601-0.0960.01870.04880.0569-0.0591-0.00390.03850.01180.1591-0.10360.04410.3433-0.05640.165914.625-30.370257.1908
20.6131-0.21660.14760.0882-0.03460.1431-0.1774-0.12820.21650.08420.0505-0.0375-0.1558-0.0307-0.09280.16530.04310.02030.05370.00570.160410.5419-26.968546.7541
30.0273-0.02610.00160.04710.01570.01440.00550.00570.0307-0.01160.00580.0108-0.016-0.0168-0.01030.09240.0930.04680.03950.09490.086114.9368-27.496742.9079
40.3980.09280.11790.02150.02940.035-0.0031-0.1434-0.09480.04270.0065-0.01250.07130.0490.02330.16950.0664-0.08370.090.03030.036224.9286-28.46752.1586
50.0604-0.06580.00460.1258-0.06870.0666-0.0159-0.00180.0376-0.0050.0151-0.006-0.0231-0.0050.0863-0.1069-0.0378-0.2021-0.07470.0746-0.039915.4709-20.863333.3761
60.1039-0.00590.02650.0033-0.00120.007-0.00130.02690.00680.0342-0.0139-0.05470.00020.1035-0.07950.14560.0285-0.14780.26410.04020.174232.4031-24.951641.4926
70.03130.02010.01710.1117-0.04340.03870.08480.005-0.094-0.1102-0.00630.05350.1628-0.01540.11040.2818-0.0056-0.08880.11510.05280.147524.7178-36.423641.5926
80.14880.1432-0.00410.1394-0.0032-0.0002-0.0045-0.04680.08050.0035-0.01370.073-0.02160.0167-0.05180.1113-0.0969-0.00050.1567-0.01450.081265.26620.351623.4481
90.12210.05120.11240.02250.03330.2574-0.02860.00350.08770.0222-0.0131-0.0237-0.07550.04010.01650.0455-0.0485-0.0080.1025-0.05240.190260.9649-2.712727.0642
100.0271-0.0506-0.00180.09530.00310.0001-0.0076-0.0091-0.056-0.0853-0.00430.06680.0639-0.009-0.02840.1305-0.03470.02840.05630.01490.147764.8538-13.93224.1077
110.08-0.00260.03980.05730.02820.0358-0.0060.064-0.0123-0.06020.0807-0.0341-0.05120.03420.20640.1087-0.10210.04870.07180.00090.068973.5178-7.09715.183
120.0766-0.01660.01290.02430.01310.01460.0153-0.00190.0243-0.02980.02330.0095-0.00540.06580.14680.1163-0.0325-0.05130.1071-0.04860.094164.4096-3.697211.2504
130.3416-0.24870.08260.1852-0.08160.1976-0.0239-0.13040.12790.0969-0.0076-0.0135-0.0252-0.0110.09730.0709-0.0491-0.0220.0767-0.02850.033453.4044-4.113123.5826
140.0258-0.0090.01770.0081-0.00880.0148-0.01610.0588-0.0061-0.0267-0.02570.0016-0.0005-0.0104-0.29890.055-0.0346-0.00330.2607-0.02870.028362.5967-9.042.8858
150.02730.02810.00310.1294-0.04120.02660.00920.0204-0.01570.02430.0179-0.1273-0.0069-0.0064-0.00980.11520.0313-0.00630.2164-0.0460.217469.8195-14.91974.4102
160.0049-0.0089-0.00220.02410.0030.00270.02360.002-0.08180.0431-0.0108-0.03490.1217-0.01790.00160.1812-0.0647-0.02090.18270.06590.324958.4122-16.540710.6897
170.0112-0.0045-0.00690.01180.00110.0046-0.04190.0086-0.0316-0.0121-0.02160.2390.0397-0.05410.00020.1686-0.04650.03130.28390.02120.238846.156-7.356713.157
180.0219-0.01430.0040.04220.00040.00530.0602-0.04720.1652-0.05320.0293-0.0749-0.08670.00910.00030.3418-0.0190.03630.1840.04580.351554.2293.478913.2161
190.0028-0.0020.00520.0477-0.04480.04620.00470.04070.0094-0.053-0.0636-0.0455-0.01010.066-0.09270.2110.0977-0.0190.41840.14470.195539.3125-2.8157-21.063
200.0127-0.0205-0.01370.03340.02160.0143-0.00290.01830.0340.0070.00690.002-0.0250.00910.02550.09260.0111-0.05240.22670.04560.200237.29111.125-11.6731
210.031-0.0137-0.06740.0408-0.01050.2293-0.04520.0304-0.06780.0223-0.0626-0.06670.0955-0.070.00020.2631-0.14880.00520.5343-0.04910.31140.1049-9.6291-18.0832
220.31760.1244-0.04490.1252-0.05660.0253-0.02180.1508-0.00760.02450.0022-0.0356-0.0575-0.0374-0.06570.06720.0618-0.04450.19370.04420.082329.8268-7.7117-7.5016
230.04470.0064-0.01560.0174-0.00830.0132-0.0073-0.02290.00360.0121-0.0239-0.00780.0031-0.0135-0.01970.11220.0177-0.0440.2759-0.00990.207237.2191-1.6063.2093
240.01290.0093-0.0090.0119-0.00060.0104-0.0044-0.0029-0.01030.00530.00890.00160.0089-0.006-0.02820.0499-0.0647-0.00720.17170.10880.101839.6883-6.0166-6.8663
250.06560.0191-0.04890.1325-0.01580.0464-0.02660.05490.0322-0.0783-0.0039-0.04430.03080.03020.03180.1311-0.04320.050.23890.13840.092549.6293-4.9646-16.2489
260.0286-0.00430.01140.1810.05210.0208-0.0786-0.0072-0.10140.0607-0.01030.06560.07150.0308-0.14710.17380.01920.03230.1230.06060.167940.3343-10.1454.7204
270.0452-0.00880.0130.0321-0.00640.0298-0.0235-0.00960.01660-0.01090.00260-0.0038-0.04560.06620.05960.0650.1047-0.02190.238932.9236-15.42533.1132
280.03210.00290.02020.1107-0.00910.0703-0.01770.0108-0.06870.004-0.01760.00590.0732-0.01810.00340.4393-0.03610.060.20240.09460.37443.9741-17.7855-3.5808
290.03020.03810.02370.05780.05570.0924-0.0122-0.00940.00390.01970.0295-0.0272-0.0050.06150.0130.13580.01850.04760.38720.06670.166457.1098-8.9005-7.4135
300.27610.10470.20560.09820.03380.188-0.034-0.01180.17510.07550.05610.1181-0.174-0.0545-0.08130.1646-0.0031-0.00570.16460.13980.230748.83692.8428-5.4417
310.1777-0.0342-0.120.06090.06050.27640.020.05360.0028-0.0324-0.0049-0.00310.00120.01410.10360.05830.0792-0.03540.2152-0.03210.052540.1745-33.195512.469
320.01150.02250.00050.0825-0.0090.0041-0.01480.0242-0.0010.0098-0.01140.0273-0.0042-0.0083-0.00140.1279-0.01650.01290.1981-0.0710.209436.5017-30.85069.2607
330.36740.0828-0.01830.0819-0.02680.2957-0.04770.18060.098-0.04730.08340.0425-0.0717-0.07980.1130.11-0.0384-0.00530.2862-0.02320.136245.6483-23.910418.1343
340.08210.0410.00920.0232-0.00510.0884-0.0176-0.016-0.02680.00390.0062-0.00470.0074-0.0074-0.01550.10750.08050.03480.1614-0.03580.167740.991-31.437132.2517
350.05830.03660.00590.02310.00380.00110.01320.00930.0120.00090.00180.0132-0.0002-0.01180.06070.0650.08730.01630.2126-0.02250.052138.7656-27.564222.0029
360.0676-0.019-0.05760.0237-0.01150.091-0.06230.0781-0.0416-0.0366-0.00650.02020.0335-0.0624-0.12590.1018-0.0416-0.0040.1214-0.13680.045428.7977-28.889612.6368
370.8437-0.45810.80280.6873-0.71380.9408-0.0969-0.05770.0894-0.0147-0.1562-0.088-0.02070.1766-0.21160.10150.01480.01240.2967-0.03180.090137.9502-22.776533.3187
380.0001-0.00310.00060.0748-0.01410.0024-0.0110.01310.0367-0.00780.00930.0018-0.0171-0.0079-0.02080.10850.0355-0.01520.06110.06150.194145.6145-17.545431.3965
390.1577-0.0832-0.03960.125-0.06650.1064-0.00010.01260.0369-0.1158-0.0094-0.13480.0090.0018-0.07830.29960.0279-0.06570.0726-0.03620.150634.2166-15.721324.6259
400.03210.0097-0.02570.14240.01070.2676-0.0215-0.03430.01570.00340.0430.0022-0.0367-0.03380.07790.15930.0861-0.02610.2445-0.04160.057921.3633-24.662721.3068
410.62990.2555-0.11550.2131-0.02320.0269-0.0201-0.0946-0.12970.09990.0181-0.00430.20120.0792-0.02420.2592-0.0590.04410.401-0.11440.213229.494-35.47623.5079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 40 )A33 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 83 )A41 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 92 )A84 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 107 )A93 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 137 )A108 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 147 )A138 - 147
7X-RAY DIFFRACTION7chain 'A' and (resid 148 through 162 )A148 - 162
8X-RAY DIFFRACTION8chain 'D' and (resid 34 through 48 )D34 - 48
9X-RAY DIFFRACTION9chain 'D' and (resid 49 through 53 )D49 - 53
10X-RAY DIFFRACTION10chain 'D' and (resid 54 through 61 )D54 - 61
11X-RAY DIFFRACTION11chain 'D' and (resid 62 through 78 )D62 - 78
12X-RAY DIFFRACTION12chain 'D' and (resid 79 through 92 )D79 - 92
13X-RAY DIFFRACTION13chain 'D' and (resid 93 through 107 )D93 - 107
14X-RAY DIFFRACTION14chain 'D' and (resid 108 through 124 )D108 - 124
15X-RAY DIFFRACTION15chain 'D' and (resid 125 through 130 )D125 - 130
16X-RAY DIFFRACTION16chain 'D' and (resid 131 through 137 )D131 - 137
17X-RAY DIFFRACTION17chain 'D' and (resid 138 through 148 )D138 - 148
18X-RAY DIFFRACTION18chain 'D' and (resid 149 through 162 )D149 - 162
19X-RAY DIFFRACTION19chain 'B' and (resid 33 through 40 )B33 - 40
20X-RAY DIFFRACTION20chain 'B' and (resid 41 through 48 )B41 - 48
21X-RAY DIFFRACTION21chain 'B' and (resid 49 through 61 )B49 - 61
22X-RAY DIFFRACTION22chain 'B' and (resid 62 through 78 )B62 - 78
23X-RAY DIFFRACTION23chain 'B' and (resid 79 through 83 )B79 - 83
24X-RAY DIFFRACTION24chain 'B' and (resid 84 through 92 )B84 - 92
25X-RAY DIFFRACTION25chain 'B' and (resid 93 through 107 )B93 - 107
26X-RAY DIFFRACTION26chain 'B' and (resid 108 through 124 )B108 - 124
27X-RAY DIFFRACTION27chain 'B' and (resid 125 through 130 )B125 - 130
28X-RAY DIFFRACTION28chain 'B' and (resid 131 through 137 )B131 - 137
29X-RAY DIFFRACTION29chain 'B' and (resid 138 through 148 )B138 - 148
30X-RAY DIFFRACTION30chain 'B' and (resid 149 through 162 )B149 - 162
31X-RAY DIFFRACTION31chain 'C' and (resid 33 through 48 )C33 - 48
32X-RAY DIFFRACTION32chain 'C' and (resid 49 through 53 )C49 - 53
33X-RAY DIFFRACTION33chain 'C' and (resid 54 through 78 )C54 - 78
34X-RAY DIFFRACTION34chain 'C' and (resid 79 through 83 )C79 - 83
35X-RAY DIFFRACTION35chain 'C' and (resid 84 through 92 )C84 - 92
36X-RAY DIFFRACTION36chain 'C' and (resid 93 through 107 )C93 - 107
37X-RAY DIFFRACTION37chain 'C' and (resid 108 through 124 )C108 - 124
38X-RAY DIFFRACTION38chain 'C' and (resid 125 through 130 )C125 - 130
39X-RAY DIFFRACTION39chain 'C' and (resid 131 through 137 )C131 - 137
40X-RAY DIFFRACTION40chain 'C' and (resid 138 through 148 )C138 - 148
41X-RAY DIFFRACTION41chain 'C' and (resid 149 through 162 )C149 - 162

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