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- PDB-8egw: Complex of Fat4(EC1-4) bound to Dchs1(EC1-3) -

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Basic information

Entry
Database: PDB / ID: 8egw
TitleComplex of Fat4(EC1-4) bound to Dchs1(EC1-3)
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 / mitral valve formation / cell migration involved in endocardial cushion formation / cell-cell adhesion via plasma-membrane adhesion molecules / hippo signaling / pattern specification process / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / post-anal tail morphogenesis / digestive tract development / catenin complex ...condensed mesenchymal cell proliferation / mitral valve formation / cell migration involved in endocardial cushion formation / cell-cell adhesion via plasma-membrane adhesion molecules / hippo signaling / pattern specification process / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / post-anal tail morphogenesis / digestive tract development / catenin complex / cell-cell junction assembly / adherens junction organization / ossification involved in bone maturation / neural tube development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / branching involved in ureteric bud morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / neurogenesis / protein localization to plasma membrane / adherens junction / cell morphogenesis / cell-cell adhesion / cerebral cortex development / apical part of cell / cadherin binding / calcium ion binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Cadherin / Laminin G domain / Laminin G domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Cadherin / Laminin G domain / Laminin G domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Calcium-binding EGF domain / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / 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 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
CACODYLATE ION / Protocadherin Fat 4 / Protocadherin-16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,23941
Polymers84,6402
Non-polymers4,59939
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-27 kcal/mol
Surface area39540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.660, 61.370, 100.966
Angle α, β, γ (deg.)90.00, 112.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protocadherin-16 / / Cadherin-19 / Cadherin-25 / Fibroblast cadherin-1 / Protein dachsous homolog 1


Mass: 33863.098 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
#2: 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

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Sugars , 4 types, 5 molecules

#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.: 2
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: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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

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Non-polymers , 4 types, 314 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Magnesium Chloride; 0.1 M Sodium Cacodylate, pH 6.1; 20% Polyethylene Glycol 1000

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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 MX-300 / Detector: CCD / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.204→49.085 Å / Num. obs: 50558 / % possible obs: 99.27 % / Redundancy: 3.4 % / CC1/2: 0.995 / Net I/σ(I): 8.87
Reflection shellResolution: 2.204→2.283 Å / Num. unique obs: 5002 / CC1/2: 0.8 / % possible all: 98.24

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A4C, 4ZPL, 4ZI8, 4ZPO, 5IU9, 3Q2W

2a4c

4zpl

4zi8

4zpo

5iu9

3q2w


Resolution: 2.3→49.083 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 2008 4.49 %
Rwork0.19 --
obs0.192 44762 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5626 0 260 292 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095973
X-RAY DIFFRACTIONf_angle_d1.0418151
X-RAY DIFFRACTIONf_dihedral_angle_d14.663585
X-RAY DIFFRACTIONf_chiral_restr0.055963
X-RAY DIFFRACTIONf_plane_restr0.0081084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.3481440.30323026X-RAY DIFFRACTION100
2.3575-2.42130.32131420.29242981X-RAY DIFFRACTION100
2.4213-2.49250.30641330.27793055X-RAY DIFFRACTION100
2.4925-2.5730.31681540.25343059X-RAY DIFFRACTION100
2.573-2.66490.3421390.26153026X-RAY DIFFRACTION100
2.6649-2.77160.31991390.26093036X-RAY DIFFRACTION100
2.7716-2.89770.3161550.25053012X-RAY DIFFRACTION100
2.8977-3.05050.31841300.22883071X-RAY DIFFRACTION100
3.0505-3.24160.25791460.21553042X-RAY DIFFRACTION100
3.2416-3.49180.22791470.18513046X-RAY DIFFRACTION100
3.4918-3.84310.2121450.1643083X-RAY DIFFRACTION100
3.8431-4.39890.24661450.15393065X-RAY DIFFRACTION100
4.3989-5.54090.16851410.14553095X-RAY DIFFRACTION100
5.5409-49.0830.17021480.16613157X-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)
10.23280.4783-0.63120.1395-0.2629-0.1553-0.1059-0.0127-0.1748-0.1031-0.0295-0.08960.1044-0.035100.4825-0.11260.04640.4680.00740.4365.25526.73476.6183
20.17690.3969-0.12040.07180.09550.4650.05940.1079-0.0331-0.05580.0074-0.0665-0.0522-0.0406-0.00040.42010.01240.07640.34850.01220.349628.7979-17.872320.1234
30.8151-0.13370.84610.3131-0.04480.9190.0814-0.33620.004-0.08660.0070.2120.19490.0565-00.3458-0.0105-0.03770.32990.03970.3268-0.8793-33.536554.4005
40.0120.2224-0.2751-0.03470.03080.4784-0.0817-0.06680.2086-0.0687-0.04130.01260.2101-0.0369-0.00020.3994-0.0490.10420.39690.0250.464-41.4911-25.425872.142
50.3792-0.08710.4120.4888-0.04990.36510.0185-0.0210.0876-0.0902-0.01830.02460.09150.056500.34250.0140.00560.30640.03440.3855-10.7778-18.201341.9869
60.12130.3102-0.31250.409-0.19460.030.04020.06280.3890.00760.07460.1654-0.0169-0.03030.00050.3196-0.0438-0.01960.38040.05520.345723.51882.255333.1783
70.19430.05640.10610.6506-0.22060.7137-0.00870.10330.36720.07380.14150.0523-0.17190.26380.00030.4879-0.10650.01630.5453-0.06090.571771.935629.268816.5294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 146 )
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 356 )
4X-RAY DIFFRACTION4chain 'B' and (resid 44 through 138 )
5X-RAY DIFFRACTION5chain 'B' and (resid 139 through 214 )
6X-RAY DIFFRACTION6chain 'B' and (resid 215 through 356 )
7X-RAY DIFFRACTION7chain 'B' and (resid 357 through 467 )

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