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- PDB-6bd4: Crystal structure of human apo-Frizzled4 receptor -

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Basic information

Entry
Database: PDB / ID: 6bd4
TitleCrystal structure of human apo-Frizzled4 receptor
ComponentsFrizzled-4/Rubredoxin chimeric protein
KeywordsMEMBRANE PROTEIN / GPCR / Frizzled / apo
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 / alkane catabolic process / regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of neuron projection arborization / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / endothelial cell differentiation / establishment of blood-brain barrier / positive regulation of dendrite morphogenesis / 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 / positive regulation of DNA-binding transcription factor activity / PDZ domain binding / Asymmetric localization of PCP proteins / sensory perception of sound / clathrin-coated endocytic vesicle membrane / 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 / electron transfer activity / response to hypoxia / cell population proliferation / cilium / positive regulation of cell migration / iron ion binding / protein heterodimerization activity / dendrite / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of DNA-templated transcription / 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 / Rubredoxin / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Rubredoxin, iron-binding site / Rubredoxin signature. / Frizzled/secreted frizzled-related protein ...Frizzled-4 / Frizzled 4, cysteine-rich domain / Rubredoxin / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Rubredoxin, iron-binding site / Rubredoxin signature. / Frizzled/secreted frizzled-related protein / Frizzled / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Single Sheet / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / Frizzled-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, S. / Wu, Y. / Pu, M. / Chen, Y. / Dong, S. / Guo, Y. / Han, G.Y. / Stevens, R.C. / Zhao, S. / Xu, F.
CitationJournal: Nature / Year: 2018
Title: Crystal structure of the Frizzled 4 receptor in a ligand-free state.
Authors: Yang, S. / Wu, Y. / Xu, T.H. / de Waal, P.W. / He, Y. / Pu, M. / Chen, Y. / DeBruine, Z.J. / Zhang, B. / Zaidi, S.A. / Popov, P. / Guo, Y. / Han, G.W. / Lu, Y. / Suino-Powell, K. / Dong, S. ...Authors: Yang, S. / Wu, Y. / Xu, T.H. / de Waal, P.W. / He, Y. / Pu, M. / Chen, Y. / DeBruine, Z.J. / Zhang, B. / Zaidi, S.A. / Popov, P. / Guo, Y. / Han, G.W. / Lu, Y. / Suino-Powell, K. / Dong, S. / Harikumar, K.G. / Miller, L.J. / Katritch, V. / Xu, H.E. / Shui, W. / Stevens, R.C. / Melcher, K. / Zhao, S. / Xu, F.
History
DepositionOct 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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 1.4Nov 20, 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/Rubredoxin chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,00718
Polymers47,8151
Non-polymers3,19217
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.670, 154.690, 114.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1214-

HOH

DetailsAuthors state that the biological unit is unknown

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Frizzled-4/Rubredoxin chimeric protein


Mass: 47814.941 Da / Num. of mol.: 1 / Mutation: M309L, C450I, C507F, S508Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: FZD4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9ULV1, UniProt: P00268

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Non-polymers , 6 types, 40 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM sodium cacodylate trihydrate (pH 6.0), 80 mM Magnesium Sulfate, 30% PEG400, 1.5-2.5% v/v (+/-)-2-Methyl-2,4-pentanediol
PH range: 6.0-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.99 Å / Num. obs: 21742 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 76.82 Å2 / CC1/2: 1 / Net I/σ(I): 18.19
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 3.52 / Num. unique obs: 2120 / CC1/2: 0.9 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JKV

4jkv


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.942 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.294 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.214
Details: THERE ARE SOME UNKNOWN DENSITIES FOR ATOMS IN THE ORTHOSTERIC BINDING SITE. THEY HAVE BEEN MODELLED AS UNX.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1344 6.18 %RANDOM
Rwork0.21 ---
obs0.211 21742 99.6 %-
Displacement parametersBiso mean: 94.42 Å2
Baniso -1Baniso -2Baniso -3
1--6.5203 Å20 Å20 Å2
2--3.5707 Å20 Å2
3---2.9497 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 178 27 3198
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073245HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.764376HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1476SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes458HARMONIC5
X-RAY DIFFRACTIONt_it3245HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion2.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion411SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4020SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.209 176 6.23 %
Rwork0.207 2649 -
all0.207 2825 -
obs--99.09 %
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)
10.68220.2360.14531.76030.01442.6226-0.01720.13240.0305-0.36210.0585-0.1031-0.10620.2366-0.04140.20490.00350.0331-0.2231-0.0223-0.303-20.75935.6268-17.5562
21.78051.8654-0.52328.3154-0.54664.50490.0795-0.07920.53480.1589-0.06230.2276-0.03090.0967-0.01720.304-0.1520.0061-0.304-0.05790.0203-44.7638-39.02173.8896
31.32290.3265-0.04911.36450.18372.88920.00070.1556-0.1604-0.13370.0608-0.27560.34750.4512-0.06150.17810.03250.0321-0.1745-0.0049-0.304-15.0816-3.1096-11.6129
40.95390.41740.33871.838-0.2051.86130.0143-0.00070.0962-0.16360.1007-0.1573-0.0020.0897-0.1150.26540.05660.0157-0.0968-0.047-0.2513-26.08012.803-16.6652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|181 - A|419 }A181 - 419
2X-RAY DIFFRACTION2{ A|1001 - A|1054 }A1001 - 1054
3X-RAY DIFFRACTION3{ A|428 - A|513 }A428 - 513
4X-RAY DIFFRACTION4{ A|1102 - A|1117 A|1201 - A|1223 }A1102 - 1117
5X-RAY DIFFRACTION4{ A|1102 - A|1117 A|1201 - A|1223 }A1201 - 1223

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