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- PDB-6cgb: chimera of mouse cadherin-11 EC1 and mouse cadherin-6 EC2 -

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Basic information

Entry
Database: PDB / ID: 6cgb
Titlechimera of mouse cadherin-11 EC1 and mouse cadherin-6 EC2
ComponentsCadherin-11, Cadherin-6 chimera
KeywordsCELL ADHESION / Cadherin EC domain Dimer Extracellular
Function / homology
Function and homology information


Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / synaptic membrane adhesion / cell-cell adhesion mediated by cadherin / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / focal adhesion assembly / catenin complex / cell-cell junction assembly ...Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / synaptic membrane adhesion / cell-cell adhesion mediated by cadherin / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / focal adhesion assembly / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / Notch signaling pathway / negative regulation of cell migration / adherens junction / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cell morphogenesis / cell adhesion / cadherin binding / glutamatergic synapse / synapse / calcium ion binding / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. ...Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Cadherin-11 / Cadherin-6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsBrasch, J. / Harrison, O.J. / Shapiro, L. / Kaeser, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM062270 United States
National Science Foundation (NSF, United States)MCB- 0918535 United States
CitationJournal: Cell Rep / Year: 2018
Title: Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior.
Authors: Brasch, J. / Katsamba, P.S. / Harrison, O.J. / Ahlsen, G. / Troyanovsky, R.B. / Indra, I. / Kaczynska, A. / Kaeser, B. / Troyanovsky, S. / Honig, B. / Shapiro, L.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-11, Cadherin-6 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1437
Polymers22,7791
Non-polymers3636
Water362
1
A: Cadherin-11, Cadherin-6 chimera
hetero molecules

A: Cadherin-11, Cadherin-6 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,28514
Polymers45,5582
Non-polymers72712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area3260 Å2
ΔGint-42 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.496, 81.030, 166.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Cadherin-11, Cadherin-6 chimera / OSF-4 / Osteoblast cadherin / OB-cadherin / Kidney cadherin / K-cadherin


Mass: 22779.195 Da / Num. of mol.: 1
Fragment: cadherin-11 EC1 (UNP residues 54-155) + cadherin-6 EC2 (UNP residues 156-260)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh11, Cad-11, Cdh6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55288, UniProt: P97326
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 4 M sodium chloride, 0.1 M sodium acetate, pH 5.5, cryoprotectant: 30% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2014
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.994→30 Å / Num. obs: 7540 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.8
Reflection shellResolution: 2.994→3.18 Å / Rmerge(I) obs: 1.766 / Num. unique obs: 720

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2A4C & 6CGU

2a4c

6cgu


Resolution: 2.994→19.681 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3005 379 5.03 %
Rwork0.2703 --
obs0.2718 7540 99.41 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.994→19.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 19 2 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041615
X-RAY DIFFRACTIONf_angle_d0.5892195
X-RAY DIFFRACTIONf_dihedral_angle_d13.141956
X-RAY DIFFRACTIONf_chiral_restr0.048252
X-RAY DIFFRACTIONf_plane_restr0.006289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9939-3.42510.39281230.39022322X-RAY DIFFRACTION99
3.4251-4.30780.37271240.30952355X-RAY DIFFRACTION100
4.3078-19.68150.25711320.23252484X-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)
13.3462-0.23241.31140.8589-0.622.23060.0435-0.68410.36720.70240.121-0.0281-1.42490.3291-0.00061.2838-0.12910.12511.5357-0.11491.0613-5.6509-8.31045.7892
23.36050.04191.48182.15580.5082.82720.40480.01960.52650.30420.10130.2843-1.15430.0256-0.0011.1822-0.0630.21790.9090.13711.61373.72999.1918-34.6866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain a and resid 1:99
2X-RAY DIFFRACTION2chain a and resid 100:207

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