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- PDB-6ne1: Designed repeat protein in complex with Fz4 -

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Basic information

Entry
Database: PDB / ID: 6ne1
TitleDesigned repeat protein in complex with Fz4
Components
  • Frizzled-4
  • Pfs, NACHT and Ankyrin domain protein
KeywordsBIOSYNTHETIC PROTEIN/SIGNALING PROTEIN / Frizzled / Designed protein / BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / retinal blood vessel morphogenesis / retina vasculature morphogenesis in camera-type eye / locomotion involved in locomotory behavior / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 ...cerebellum vasculature morphogenesis / Wnt signaling pathway, calcium modulating pathway / Norrin signaling pathway / extracellular matrix-cell signaling / progesterone secretion / retinal blood vessel morphogenesis / retina vasculature morphogenesis in camera-type eye / locomotion involved in locomotory behavior / Signaling by RNF43 mutants / WNT5A-dependent internalization of FZD4 / regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of neuron projection arborization / Wnt receptor activity / non-canonical Wnt signaling pathway / endothelial cell differentiation / Wnt-protein binding / positive regulation of dendrite morphogenesis / establishment of blood-brain barrier / Class B/2 (Secretin family receptors) / cytokine receptor activity / cytokine binding / negative regulation of cell-substrate adhesion / canonical Wnt signaling pathway / vasculogenesis / cellular response to retinoic acid / Regulation of FZD by ubiquitination / substrate adhesion-dependent cell spreading / cellular response to leukemia inhibitory factor / Asymmetric localization of PCP proteins / PDZ domain binding / clathrin-coated endocytic vesicle membrane / sensory perception of sound / G protein-coupled receptor activity / Wnt signaling pathway / neuron differentiation / cell-cell junction / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / amyloid-beta binding / Ca2+ pathway / angiogenesis / response to hypoxia / cell population proliferation / cilium / positive regulation of cell migration / protein heterodimerization activity / dendrite / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane
Similarity search - Function
Frizzled-4 / Frizzled 4, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled 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-4 / Frizzled 4, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Neosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.011 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 15, 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 1.4Jul 29, 2020Group: 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 1.5Oct 11, 2023Group: 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
Revision 1.6Nov 6, 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-4
B: Pfs, NACHT and Ankyrin domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0104
Polymers33,5682
Non-polymers4422
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-11 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.846, 62.611, 86.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Frizzled-4 / hFz4 / FzE4


Mass: 13619.851 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9ULV1
#2: Protein Pfs, NACHT and Ankyrin domain protein


Mass: 19947.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_1G01020 / Production host: Escherichia coli (E. coli)
#3: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, pH 6.3 and 20% PEG3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→50 Å / Num. obs: 5867 / % possible obs: 98.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 10
Reflection shellResolution: 3.01→3.12 Å / Rmerge(I) obs: 0.687 / Num. unique obs: 542

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPB

5bpb


Resolution: 3.011→44.431 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.93
RfactorNum. reflection% reflection
Rfree0.2928 587 10.01 %
Rwork0.2339 --
obs0.2404 5864 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.011→44.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 28 6 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032099
X-RAY DIFFRACTIONf_angle_d0.5962855
X-RAY DIFFRACTIONf_dihedral_angle_d9.6311273
X-RAY DIFFRACTIONf_chiral_restr0.039341
X-RAY DIFFRACTIONf_plane_restr0.004368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0112-3.31420.37191380.31541244X-RAY DIFFRACTION96
3.3142-3.79350.33281450.25791304X-RAY DIFFRACTION100
3.7935-4.77850.29461490.22151335X-RAY DIFFRACTION100
4.7785-44.4360.25551550.21131394X-RAY DIFFRACTION99
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)
14.43750.8958-0.81064.54540.36914.8219-0.0270.36390.3509-0.60180.1951-0.0929-0.1677-0.1534-0.18180.58710.02290.0390.4935-0.05460.4802-5.8528-9.917112.2949
23.0763-0.0262-0.29474.1590.99993.72180.066-0.2006-0.16960.1703-0.1806-0.20460.0869-0.41560.08420.3916-0.0047-0.00870.51660.03640.3555-16.3791-21.400728.5778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 44 through 161)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 161)

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