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- PDB-8egx: Complex of Fat4(EC1-4) bound to Dchs1(EC1-4) -

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Basic information

Entry
Database: PDB / ID: 8egx
TitleComplex of Fat4(EC1-4) bound to Dchs1(EC1-4)
Components
  • Protocadherin Fat 4
  • Protocadherin-16
KeywordsCELL ADHESION / Fat4 / Dachsous1 / Cadherin / Protocadherin / Adhesion / Fat / Dachsous
Function / homology
Function and homology information


condensed mesenchymal cell proliferation / septin cytoskeleton organization / mitral valve formation / cell migration involved in endocardial cushion formation / : / calcium-dependent cell-cell adhesion / hippo signaling / pattern specification process / post-anal tail morphogenesis / catenin complex ...condensed mesenchymal cell proliferation / septin cytoskeleton organization / mitral valve formation / cell migration involved in endocardial cushion formation / : / calcium-dependent cell-cell adhesion / hippo signaling / pattern specification process / post-anal tail morphogenesis / catenin complex / digestive tract development / heterophilic cell-cell adhesion / neural tube development / ossification involved in bone maturation / branching involved in ureteric bud morphogenesis / homophilic cell-cell adhesion / cochlea development / neurogenesis / protein localization to plasma membrane / cell-cell adhesion / beta-catenin binding / cerebral cortex development / apical part of cell / cell migration / gene expression / cadherin binding / calcium ion binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
FAT4-like, N-terminal cadherin-like domain / : / Laminin G domain / EGF-like, conserved site / Cadherin / Human growth factor-like EGF / Laminin G domain profile. / Cadherins / Laminin G domain / Laminin G domain ...FAT4-like, N-terminal cadherin-like domain / : / Laminin G domain / EGF-like, conserved site / Cadherin / Human growth factor-like EGF / Laminin G domain profile. / Cadherins / Laminin G domain / Laminin G domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / : / Calcium-binding EGF domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protocadherin Fat 4 / Protocadherin-16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.688 Å
AuthorsMedina, E. / Luca, V.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133482 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure of the planar cell polarity cadherins Fat4 and Dachsous1.
Authors: Medina, E. / Easa, Y. / Lester, D.K. / Lau, E.K. / Sprinzak, D. / Luca, V.C.
History
DepositionSep 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protocadherin Fat 4
A: Protocadherin-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,77125
Polymers95,7412
Non-polymers2,03123
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-70 kcal/mol
Surface area44770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.222, 82.102, 224.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protocadherin Fat 4 / hFat4 / Cadherin family member 14 / FAT tumor suppressor homolog 4 / Fat-like cadherin protein FAT-J


Mass: 50777.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAT4, CDHF14, FATJ, Nbla00548 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6V0I7
#2: Protein Protocadherin-16 / Cadherin-19 / Cadherin-25 / Fibroblast cadherin-1 / Protein dachsous homolog 1


Mass: 44963.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCHS1, CDH19, CDH25, FIB1, KIAA1773, PCDH16 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96JQ0
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 4 / Source method: obtained synthetically / 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
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.5; 0.2 M Sodium Chloride; 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.688→49.35 Å / Num. obs: 12968 / % possible obs: 95.9 % / Redundancy: 2 % / CC1/2: 0.994 / Net I/σ(I): 4.05
Reflection shellResolution: 3.688→3.82 Å / Num. unique obs: 1214 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EGW, 6VFT

8egw

6vft


Resolution: 3.688→49.35 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 620 4.81 %
Rwork0.2708 12279 -
obs0.2722 12899 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.87 Å2 / Biso mean: 72.4536 Å2 / Biso min: 22.23 Å2
Refinement stepCycle: final / Resolution: 3.688→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 102 0 6485
Biso mean--84.83 --
Num. residues----846
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.688-4.05850.34081490.3212291493
4.0585-4.64540.30541460.2602304497
4.6454-5.85120.30421680.2675307797
5.8512-49.350.26911570.2565324497

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