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- PDB-6cg7: mouse cadherin-22 EC1-2 adhesive fragment -

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Basic information

Entry
Database: PDB / ID: 6cg7
Titlemouse cadherin-22 EC1-2 adhesive fragment
ComponentsCadherin-22
KeywordsCELL ADHESION / Cadherin EC domain Dimer Extracellular
Function / homology
Function and homology information


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 / adherens junction / cell morphogenesis / beta-catenin binding / cell migration ...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 / adherens junction / cell morphogenesis / beta-catenin binding / cell migration / 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 / Cadherin-like ...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 / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 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 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 ...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_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cadherin-22
B: Cadherin-22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8458
Polymers45,6042
Non-polymers2406
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-42 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.260, 45.077, 128.054
Angle α, β, γ (deg.)90.00, 92.25, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Cadherin-22 / Pituitary and brain cadherin / PB-cadherin


Mass: 22802.074 Da / Num. of mol.: 2 / Fragment: EC1-2 (UNP residues 60-266)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WTP5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17% v/v PEG6000, 0.1 M HEPES, pH 7.0, 5% ethylene glycol, cryoprotectant: 30% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2011
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 15707 / % possible obs: 98.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.496 / Num. unique obs: 1480

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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 6CGU

6cgu


Resolution: 2.705→19.927 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2772 1572 10.01 %
Rwork0.2261 --
obs0.2312 15707 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.705→19.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 6 10 3227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023273
X-RAY DIFFRACTIONf_angle_d0.5254454
X-RAY DIFFRACTIONf_dihedral_angle_d12.4541940
X-RAY DIFFRACTIONf_chiral_restr0.048507
X-RAY DIFFRACTIONf_plane_restr0.003588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7048-2.79180.47581320.42011218X-RAY DIFFRACTION93
2.7918-2.89130.36631290.34641226X-RAY DIFFRACTION97
2.8913-3.00670.42531410.3471271X-RAY DIFFRACTION97
3.0067-3.14310.41481380.34881273X-RAY DIFFRACTION98
3.1431-3.30810.35111490.32441260X-RAY DIFFRACTION98
3.3081-3.51430.33271460.27871283X-RAY DIFFRACTION99
3.5143-3.78390.28831450.2571293X-RAY DIFFRACTION100
3.7839-4.16160.31131460.20851317X-RAY DIFFRACTION100
4.1616-4.75660.23591470.18961301X-RAY DIFFRACTION100
4.7566-5.9660.22011430.17551325X-RAY DIFFRACTION100
5.966-19.92790.19641560.16451368X-RAY DIFFRACTION99

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