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- PDB-2a4c: Crystal structure of mouse cadherin-11 EC1 -

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Basic information

Entry
Database: PDB / ID: 2a4c
TitleCrystal structure of mouse cadherin-11 EC1
ComponentsCadherin-11
KeywordsCELL ADHESION / Cadherin / Extracellular domain / Dimer
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 / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cell morphogenesis / cell adhesion / cadherin binding / glutamatergic synapse / 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: 2.9 Å
AuthorsPatel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Schieren, I. / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-11
B: Cadherin-11


Theoretical massNumber of molelcules
Total (without water)22,1262
Polymers22,1262
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-18 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.937, 76.937, 102.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 1 - 98 / Label seq-ID: 2 - 99

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 11063.200 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 68.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→66.667 Å / Num. obs: 8099 / % possible obs: 99.9 %
Reflection shellResolution: 2.9→3 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EC1 domain from PDB ID 2A4E

2a4e


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 29.584 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.641 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 374 4.6 %RANDOM
Rwork0.204 ---
all0.206 ---
obs-7706 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.282 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å21.57 Å20 Å2
2--3.14 Å20 Å2
3----4.7 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 0 17 1579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221596
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9492170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0485196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44724.87882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69115258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7431510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021250
X-RAY DIFFRACTIONr_nbd_refined0.2280.2653
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.21
X-RAY DIFFRACTIONr_mcbond_it0.3981.5999
X-RAY DIFFRACTIONr_mcangle_it0.72221592
X-RAY DIFFRACTIONr_scbond_it1.223669
X-RAY DIFFRACTIONr_scangle_it2.034.5578
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 775 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.44MEDIUM POSITIONAL0.5
0.57MEDIUM THERMAL2
LS refinement shellResolution: 2.9→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 25 -
Rwork0.304 565 -
all-590 -
obs--100 %
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)
11.31060.16351.00734.67140.21962.49540.0522-0.214-0.10970.14860.1212-0.1069-0.30560.0783-0.1734-0.1117-0.003-0.0299-0.03840.0036-0.107740.8109-5.9927-25.6711
23.7247-2.3092-0.81652.8668-2.02886.20190.2324-0.18580.27360.41260.02930.1203-0.3554-0.086-0.26170.00460.03640.0028-0.07210.0289-0.055242.3216-18.2601-10.7385
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 2 - 98 / Label seq-ID: 3 - 99

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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