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- PDB-6cgs: mouse cadherin-7 EC1-2 adhesive fragment -

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Basic information

Entry
Database: PDB / ID: 6cgs
Titlemouse cadherin-7 EC1-2 adhesive fragment
ComponentsCadherin-7
KeywordsCELL ADHESION / Cadherin EC domain Dimer Extracellular
Function / homology
Function and homology information


Adherens junctions interactions / multicellular organism development / cell-cell adhesion via plasma-membrane adhesion molecules / 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 / adherens junction / cell morphogenesis ...Adherens junctions interactions / multicellular organism development / cell-cell adhesion via plasma-membrane adhesion molecules / 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 / adherens junction / cell morphogenesis / membrane => GO:0016020 / cadherin binding / calcium ion binding
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: 1.72 Å
AuthorsBrasch, J. / Harrison, O.J. / Kaczynska, A. / 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-7
B: Cadherin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8699
Polymers45,5372
Non-polymers3337
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-45 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.304, 82.431, 93.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cadherin-7


Mass: 22768.279 Da / Num. of mol.: 2 / Fragment: EC1-2 (UNP residues 48-254)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BM92
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 21.5% (w/v) PEG 6000 0.1M MES pH 5.6 1M LiCl 30% glycerol (cryoprotectant)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 48271 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.33
Reflection shellResolution: 1.7→1.78 Å / Rmerge(I) obs: 0.656 / Num. unique obs: 4704

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Processing

Software
NameVersionClassification
PHENIXDEV_1839refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CGU

6cgu


Resolution: 1.72→20 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.87
RfactorNum. reflection% reflection
Rfree0.199 2414 5 %
Rwork0.16 --
obs0.162 48266 99.8 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 1.72→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 12 659 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093482
X-RAY DIFFRACTIONf_angle_d1.34780
X-RAY DIFFRACTIONf_dihedral_angle_d13.1981347
X-RAY DIFFRACTIONf_chiral_restr0.144541
X-RAY DIFFRACTIONf_plane_restr0.005632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7223-1.75740.24631370.21862617X-RAY DIFFRACTION99
1.7574-1.79560.22891380.20682644X-RAY DIFFRACTION99
1.7956-1.83740.25121430.20122692X-RAY DIFFRACTION100
1.8374-1.88330.23791390.18722650X-RAY DIFFRACTION100
1.8833-1.93420.23071400.17562657X-RAY DIFFRACTION100
1.9342-1.9910.2451400.17552657X-RAY DIFFRACTION100
1.991-2.05520.21431420.16812666X-RAY DIFFRACTION100
2.0552-2.12860.21341410.16292682X-RAY DIFFRACTION100
2.1286-2.21370.20261400.15822671X-RAY DIFFRACTION100
2.2137-2.31430.20951410.16142686X-RAY DIFFRACTION100
2.3143-2.43620.18771430.1622692X-RAY DIFFRACTION100
2.4362-2.58850.20911420.16142718X-RAY DIFFRACTION100
2.5885-2.78790.22231420.16992694X-RAY DIFFRACTION100
2.7879-3.06750.20721440.16552742X-RAY DIFFRACTION100
3.0675-3.50930.18921430.15222716X-RAY DIFFRACTION100
3.5093-4.41350.17411470.12862784X-RAY DIFFRACTION100
4.4135-19.99650.16731520.15652884X-RAY DIFFRACTION100

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