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- PDB-6ndz: Designed repeat protein in complex with Fz8 -

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Basic information

Entry
Database: PDB / ID: 6ndz
TitleDesigned repeat protein in complex with Fz8
Components
  • Designed repeat binding protein
  • Frizzled-8
KeywordsBIOSYNTHETIC PROTEIN/SIGNALING PROTEIN / Frizzled / Designed protein / BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Wnt-Frizzled-LRP5/6 complex / Signaling by RNF43 mutants / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / neuronal dense core vesicle / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins ...Wnt-Frizzled-LRP5/6 complex / Signaling by RNF43 mutants / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / neuronal dense core vesicle / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / G protein-coupled receptor activity / PDZ domain binding / neuron differentiation / T cell differentiation in thymus / angiogenesis / positive regulation of protein phosphorylation / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / membrane / 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. / Ankyrin repeat-containing domain / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / ACETIC ACID / Frizzled-8
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.264 Å
AuthorsMiao, Y. / Jude, K.M. / Garcia, K.C.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Frizzled-8
B: Designed repeat binding protein
C: Frizzled-8
D: Designed repeat binding protein
E: Frizzled-8
F: Designed repeat binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,22616
Polymers106,3976
Non-polymers82910
Water3,873215
1
A: Frizzled-8
B: Designed repeat binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17610
Polymers35,4662
Non-polymers7108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-50 kcal/mol
Surface area13760 Å2
MethodPISA
2
C: Frizzled-8
D: Designed repeat binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5253
Polymers35,4662
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-20 kcal/mol
Surface area13810 Å2
MethodPISA
3
E: Frizzled-8
F: Designed repeat binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5263
Polymers35,4662
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-20 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.930, 109.015, 114.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Frizzled-8 / / hFz8


Mass: 14602.736 Da / Num. of mol.: 3 / Mutation: N49Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H461
#2: Protein Designed repeat binding protein


Mass: 20862.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 225 molecules

#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M HEPE, pH 7.5 and 55% MPD

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 44492 / % possible obs: 94.1 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.5
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 0.748 / Num. unique obs: 3389

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F0A

4f0a


Resolution: 2.264→42.778 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.06
RfactorNum. reflection% reflection
Rfree0.2377 1998 4.49 %
Rwork0.2118 --
obs0.213 44467 94.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.264→42.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 56 216 7283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037205
X-RAY DIFFRACTIONf_angle_d0.9329756
X-RAY DIFFRACTIONf_dihedral_angle_d12.3734431
X-RAY DIFFRACTIONf_chiral_restr0.0411094
X-RAY DIFFRACTIONf_plane_restr0.0051271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2645-2.32110.3811020.29732193X-RAY DIFFRACTION69
2.3211-2.38380.3311180.2892613X-RAY DIFFRACTION83
2.3838-2.4540.31371350.28162729X-RAY DIFFRACTION86
2.454-2.53320.3511380.26492833X-RAY DIFFRACTION89
2.5332-2.62370.29451420.26352973X-RAY DIFFRACTION94
2.6237-2.72870.29421440.26263144X-RAY DIFFRACTION98
2.7287-2.85290.31741490.27053189X-RAY DIFFRACTION100
2.8529-3.00330.28351550.25463172X-RAY DIFFRACTION100
3.0033-3.19140.27751480.24433207X-RAY DIFFRACTION100
3.1914-3.43770.24971500.23253210X-RAY DIFFRACTION100
3.4377-3.78350.2221500.19383248X-RAY DIFFRACTION100
3.7835-4.33050.19461530.18013241X-RAY DIFFRACTION100
4.3305-5.45420.22061520.18883291X-RAY DIFFRACTION100
5.4542-42.7860.20131620.18873426X-RAY DIFFRACTION100
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)
11.8992-0.1434-0.55740.58740.34243.2036-0.03830.0784-0.20440.0323-0.1052-0.02040.1594-0.1063-0.00030.39250.0164-0.00550.2804-0.00910.3919173.9789325.0107-1.971
21.3932-0.78871.08021.8933-1.02832.7219-0.0039-0.07550.13770.0194-0.1687-0.04650.05350.14300.35790.03110.03330.4156-0.00470.4049175.0995336.62717.7225
33.5251-0.1643-0.24432.49870.58940.35150.04120.32250.1675-0.0986-0.0647-0.03830.1380.110.00010.34430.0617-0.03040.41990.01260.3149200.6967325.9935-10.4608
42.2754-1.35970.38733.5442-0.08510.71220.18650.1332-0.5002-0.0317-0.29270.18050.35150.2539-00.54210.12010.01050.50940.0490.6506202.349303.3372-9.5109
51.8098-0.6201-0.20431.52361.20390.7042-0.0253-0.2774-0.11820.0210.06890.1225-0.01220.04080.00010.396-0.04110.00870.59970.12550.454212.3907320.63951.3757
60.8506-0.76410.02742.4385-0.10942.06470.25280.1121-0.2025-0.59010.0610.50130.2189-0.36930.00340.6236-0.1077-0.19320.68930.08030.5416211.8951309.711831.0877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 126)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 190)
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 125)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 190)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 125)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 189)

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