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- PDB-2a4e: Crystal structure of mouse cadherin-11 EC1-2 -

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Basic information

Entry
Database: PDB / ID: 2a4e
TitleCrystal structure of mouse cadherin-11 EC1-2
ComponentsCadherin-11
KeywordsCELL ADHESION / cadherin / dimer / calcium binding
Function / homology
Function and homology information


Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / 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 ...Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / 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 / negative regulation of cell migration / adherens junction / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cell morphogenesis / cell adhesion / cadherin binding / synapse / glutamatergic synapse / calcium ion binding / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPatel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Arkus, N. / Rajebhosale, M. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Type II cadherin ectodomain structures: implications for classical cadherin specificity.
Authors: Patel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Rajebhosale, M. / Arkus, N. / Schieren, I. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L.
History
DepositionJun 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif / struct_site
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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cadherin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9074
Polymers23,7871
Non-polymers1203
Water27015
1
A: Cadherin-11
hetero molecules

A: Cadherin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8158
Polymers47,5742
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_767-x+2,-x+y+1,-z+7/31
Unit cell
Length a, b, c (Å)203.249, 203.249, 42.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Cadherin-11 / / Osteoblast-cadherin / OB-cadherin / OSF-4


Mass: 23787.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh11, Cad-11 / Plasmid: pSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P55288
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 5.37 Å3/Da / Density % sol: 77.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, hepes, sucrose, calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 8610 / % possible obs: 99.9 %
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain.

1zvn

1zxk

1ncj

1edh

1l3w


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.907 / SU B: 31.513 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.621 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 433 4.8 %RANDOM
Rwork0.211 ---
all0.213 ---
obs-8536 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 3 15 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221647
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9512243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98425.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.8315265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.619158
X-RAY DIFFRACTIONr_chiral_restr0.1140.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021278
X-RAY DIFFRACTIONr_nbd_refined0.2570.2777
X-RAY DIFFRACTIONr_nbtor_refined0.3280.21127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.265
X-RAY DIFFRACTIONr_metal_ion_refined0.2010.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.26
X-RAY DIFFRACTIONr_mcbond_it0.6261.51041
X-RAY DIFFRACTIONr_mcangle_it1.13121678
X-RAY DIFFRACTIONr_scbond_it1.5423659
X-RAY DIFFRACTIONr_scangle_it2.6834.5565
LS refinement shellResolution: 3.2→3.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 38 -
Rwork0.298 582 -
all-620 -
obs--94.66 %
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)
15.1873-0.9071-1.22974.6112-1.4482.9963-0.31990.70540.1109-0.1625-0.0504-0.6908-0.17470.01720.3702-0.2544-0.1732-0.0612-0.0722-0.1005-0.0339150.856106.31244.761
213.59272.06745.68123.54140.25557.5510.36520.00340.1056-0.1306-0.15210.0430.38010.0273-0.2131-0.22950.0299-0.11290.1123-0.0995-0.4663106.119107.05333.527
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 972 - 98
22100 - 207101 - 208

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