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- PDB-6ne4: Designed repeat protein specifically in complex with Fz7CRD -

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Basic information

Entry
Database: PDB / ID: 6ne4
TitleDesigned repeat protein specifically in complex with Fz7CRD
Components
  • Designed repeat binding protein
  • Frizzled-7
KeywordsBIOSYNTHETIC 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 / somatic stem cell division / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / non-canonical Wnt signaling pathway / mesenchymal to epithelial transition / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping ...negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / somatic stem cell division / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / non-canonical Wnt signaling pathway / mesenchymal to epithelial transition / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Class B/2 (Secretin family receptors) / regulation of canonical Wnt signaling pathway / Wnt signaling pathway, planar cell polarity pathway / stem cell population maintenance / positive regulation of phosphorylation / negative regulation of cell-substrate adhesion / canonical Wnt signaling pathway / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / Asymmetric localization of PCP proteins / positive regulation of JNK cascade / PDZ domain binding / G protein-coupled receptor activity / recycling endosome membrane / neuron differentiation / T cell differentiation in thymus / positive regulation of MAPK cascade / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / membrane / plasma membrane
Similarity search - Function
Frizzled-7, cysteine-rich Wnt-binding 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-7, cysteine-rich Wnt-binding 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
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.648 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 16, 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Designed repeat binding protein
A: Frizzled-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,54418
Polymers35,0752
Non-polymers1,46916
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-198 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.604, 68.367, 86.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

21B-447-

HOH

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Components

#1: Protein Designed repeat binding protein


Mass: 20963.748 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na2HPO4, citric acid, pH 4.2 and 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.648→50 Å / Num. obs: 41862 / % possible obs: 99.6 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 38.1
Reflection shellResolution: 1.648→1.71 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 4055

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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: 5T44

5t44


Resolution: 1.648→34.578 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.88
RfactorNum. reflection% reflection
Rfree0.1861 2000 4.78 %
Rwork0.1598 --
obs0.1611 41817 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.648→34.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 78 274 2697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142468
X-RAY DIFFRACTIONf_angle_d1.3293353
X-RAY DIFFRACTIONf_dihedral_angle_d14.0881488
X-RAY DIFFRACTIONf_chiral_restr0.081372
X-RAY DIFFRACTIONf_plane_restr0.009434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6478-1.6890.25351370.21992714X-RAY DIFFRACTION97
1.689-1.73470.23641410.18992820X-RAY DIFFRACTION100
1.7347-1.78570.19071410.18012816X-RAY DIFFRACTION100
1.7857-1.84340.22461400.16922795X-RAY DIFFRACTION100
1.8434-1.90920.20141430.16572824X-RAY DIFFRACTION100
1.9092-1.98570.20851420.15882820X-RAY DIFFRACTION100
1.9857-2.0760.17921420.16242832X-RAY DIFFRACTION100
2.076-2.18550.18681420.15642827X-RAY DIFFRACTION100
2.1855-2.32240.20091410.16212825X-RAY DIFFRACTION100
2.3224-2.50160.20431430.15922850X-RAY DIFFRACTION100
2.5016-2.75330.20231440.16252869X-RAY DIFFRACTION100
2.7533-3.15150.19831450.1632874X-RAY DIFFRACTION100
3.1515-3.96960.16711460.14582910X-RAY DIFFRACTION100
3.9696-34.58590.16251530.15813041X-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)
10.6912-0.05660.26530.4399-0.11960.82130.02430.05630.0272-0.01820.03950.04880.0229-0.1243-00.1763-0.0020.00580.21840.01450.1924-109.7148-329.2771174.8113
20.73080.38-0.80470.7598-0.45870.67030.12780.01380.0680.0674-0.0556-0.0423-0.13580.08660.08570.2137-0.01920.01290.1679-0.0030.1922-88.3181-324.9176167.3216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid -1 through 192)
2X-RAY DIFFRACTION2(chain 'A' and resid 2 through 120)

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