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- PDB-6cgu: mouse cadherin-6 EC1-2 adhesive fragment -

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Basic information

Entry
Database: PDB / ID: 6cgu
Titlemouse cadherin-6 EC1-2 adhesive fragment
ComponentsCadherin-6
KeywordsCELL ADHESION / Cadherin EC domain Dimer Extracellular
Function / homology
Function and homology information


Adherens junctions interactions / synaptic membrane adhesion / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / Notch signaling pathway / adherens junction ...Adherens junctions interactions / synaptic membrane adhesion / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / Notch signaling pathway / adherens junction / cell morphogenesis / cadherin binding / glutamatergic synapse / synapse / calcium ion binding / nucleoplasm / plasma membrane
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrasch, J. / Harrison, O.J. / Shapiro, L.
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 20, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cadherin-6
B: Cadherin-6
C: Cadherin-6
D: Cadherin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,12418
Polymers92,5624
Non-polymers56114
Water21,3661186
1
A: Cadherin-6
D: Cadherin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5629
Polymers46,2812
Non-polymers2817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-60 kcal/mol
Surface area21800 Å2
MethodPISA
2
B: Cadherin-6
C: Cadherin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5629
Polymers46,2812
Non-polymers2817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-61 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.348, 141.647, 142.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Cadherin-6 / / Kidney cadherin / K-cadherin


Mass: 23140.623 Da / Num. of mol.: 4 / Fragment: EC1-2 (UNP residues 54-260)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh6 / Production host: Escherichia coli (E. coli) / References: UniProt: P97326
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1186 / 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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 18.5% (w/v) PEG 3350 0.2M sodium acetate 30% ethylene glycol (cryoprotectant)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 90099 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 23.8
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.553 / Num. unique obs: 8705

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LND

3lnd


Resolution: 1.9→19.93 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.201 4519 5.02 %
Rwork0.161 --
obs0.163 90099 99.7 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 14 1186 7708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036755
X-RAY DIFFRACTIONf_angle_d0.6529196
X-RAY DIFFRACTIONf_dihedral_angle_d13.6764070
X-RAY DIFFRACTIONf_chiral_restr0.051028
X-RAY DIFFRACTIONf_plane_restr0.0041218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9017-1.92330.28041580.25062520X-RAY DIFFRACTION90
1.9233-1.94590.25981610.22582820X-RAY DIFFRACTION100
1.9459-1.96960.26771440.21062832X-RAY DIFFRACTION100
1.9696-1.99450.22951360.2052846X-RAY DIFFRACTION100
1.9945-2.02070.24751570.20342842X-RAY DIFFRACTION100
2.0207-2.04840.24211510.19852822X-RAY DIFFRACTION100
2.0484-2.07760.24191450.18912847X-RAY DIFFRACTION100
2.0776-2.10860.22321570.19122850X-RAY DIFFRACTION100
2.1086-2.14150.22531680.18612787X-RAY DIFFRACTION100
2.1415-2.17660.27041430.1842855X-RAY DIFFRACTION100
2.1766-2.2140.21191570.17912852X-RAY DIFFRACTION100
2.214-2.25420.25051420.18262844X-RAY DIFFRACTION100
2.2542-2.29750.22981450.17782851X-RAY DIFFRACTION100
2.2975-2.34440.18531540.17192851X-RAY DIFFRACTION100
2.3444-2.39530.21241650.16722832X-RAY DIFFRACTION100
2.3953-2.45090.19981470.17132850X-RAY DIFFRACTION100
2.4509-2.51210.23071370.17022876X-RAY DIFFRACTION100
2.5121-2.57980.2011590.16672823X-RAY DIFFRACTION100
2.5798-2.65560.20661490.16022871X-RAY DIFFRACTION100
2.6556-2.74110.20951390.17482866X-RAY DIFFRACTION100
2.7411-2.83880.23231520.16432865X-RAY DIFFRACTION100
2.8388-2.95210.22381650.16772855X-RAY DIFFRACTION100
2.9521-3.0860.2311380.16922879X-RAY DIFFRACTION100
3.086-3.24810.22191440.1672889X-RAY DIFFRACTION100
3.2481-3.45060.21881470.16252883X-RAY DIFFRACTION100
3.4506-3.71540.17471660.15032865X-RAY DIFFRACTION100
3.7154-4.08640.18691330.13892919X-RAY DIFFRACTION100
4.0864-4.67110.16551540.12372917X-RAY DIFFRACTION100
4.6711-5.86010.14321430.13142937X-RAY DIFFRACTION100
5.8601-19.9270.16411630.15613034X-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)
11.1496-0.84680.77842.6669-0.20321.41120.1134-0.0533-0.0149-0.4965-0.14250.1802-0.0564-0.19630.04480.30760.056-0.03580.40040.08990.3308-47.064114.375413.9853
22.6965-0.54460.42332.8180.14811.99090.22050.2504-0.0356-0.2007-0.1448-0.24840.20330.2627-0.03760.22940.0476-0.01050.20570.00950.21437.0355-9.67588.1998
32.17480.0152-1.90011.40830.64053.12970.1973-0.12930.17270.1727-0.03540.0559-0.2128-0.0321-0.11490.3220.0430.03890.2760.01560.2475-30.77723.737652.1547
41.2359-0.25590.18461.6062-0.77030.95380.88331.3234-0.7926-0.6379-0.6942-0.11080.88350.60.06090.58150.3782-0.13520.637-0.17140.48831.2384-23.401346.582
50.39970.8171-0.9222.5659-1.49812.0410.028-0.068-0.02260.047-0.00240.05760.2654-0.0676-0.01240.3154-0.0366-0.0160.340.10270.3288-38.9909-15.146548.2399
61.7252-0.0106-0.04120.90870.00481.41340.004-0.02090.0259-0.06710.06240.1424-0.1546-0.1699-0.07090.26350.05190.03110.24080.04810.2647-26.944421.350412.1275
71.50480.3698-0.76061.1143-0.4132.63040.0481-0.0509-0.0368-0.0099-0.0478-0.0936-0.21950.26490.00780.28670.01280.06890.20650.01570.283-8.893727.81111.7131
81.5509-0.3885-0.19871.94320.53361.46490.1327-0.12960.17150.1499-0.09410.1315-0.0052-0.1841-0.03270.24780.01410.03390.37660.06770.2903-35.57193.664950.7498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 100:207
2X-RAY DIFFRACTION2CHAIN B AND RESID 100:207
3X-RAY DIFFRACTION3CHAIN C AND RESID 100:207
4X-RAY DIFFRACTION4CHAIN D AND RESID 100:207
5X-RAY DIFFRACTION5CHAIN A AND RESID 1:99
6X-RAY DIFFRACTION6CHAIN B AND RESID 1:99
7X-RAY DIFFRACTION7CHAIN C AND RESID 1:99
8X-RAY DIFFRACTION8CHAIN D AND RESID 1:99

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