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- PDB-3ubf: Crystal structure of Drosophila N-cadherin EC1-3, I -

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Basic information

Entry
Database: PDB / ID: 3ubf
TitleCrystal structure of Drosophila N-cadherin EC1-3, I
ComponentsNeural-cadherin
KeywordsCELL ADHESION / cadherin
Function / homology
Function and homology information


R8 cell development / R7 cell development / ommatidial rotation / regulation of axon extension involved in axon guidance / axon target recognition / negative regulation of dendrite morphogenesis / axon extension involved in axon guidance / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex ...R8 cell development / R7 cell development / ommatidial rotation / regulation of axon extension involved in axon guidance / axon target recognition / negative regulation of dendrite morphogenesis / axon extension involved in axon guidance / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / axon extension / axonal fasciculation / cell-cell junction assembly / adherens junction organization / regulation of dendrite morphogenesis / retinal ganglion cell axon guidance / homophilic cell adhesion via plasma membrane adhesion molecules / adherens junction / axon guidance / cell-cell adhesion / cell-cell junction / cadherin binding / axon / calcium ion binding / dendrite / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Laminin G domain / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Laminin G domain profile. / Cadherins / Cadherin / Laminin G domain / Laminin G domain / Cadherin conserved site ...Laminin G domain / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Laminin G domain profile. / Cadherins / Cadherin / Laminin G domain / Laminin G domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJin, X. / Walker, M.A. / Shapiro, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca2+-free interdomain linkers.
Authors: Jin, X. / Walker, M.A. / Felsovalyi, K. / Vendome, J. / Bahna, F. / Mannepalli, S. / Cosmanescu, F. / Ahlsen, G. / Honig, B. / Shapiro, L.
History
DepositionOct 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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: Neural-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,14820
Polymers35,9311
Non-polymers1,21719
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neural-cadherin
hetero molecules

A: Neural-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,29740
Polymers71,8622
Non-polymers2,43538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+2/31
Buried area3500 Å2
ΔGint-750 kcal/mol
Surface area32170 Å2
MethodPISA
3
A: Neural-cadherin
hetero molecules

A: Neural-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,29740
Polymers71,8622
Non-polymers2,43538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area5190 Å2
ΔGint-838 kcal/mol
Surface area30680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.289, 96.289, 148.196
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 Neural-cadherin / Cadherin-N / dN-cadherin


Mass: 35931.059 Da / Num. of mol.: 1 / Fragment: unp residues 439-753
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CadN, CG7100 / Production host: Escherichia coli (E. coli) / References: UniProt: O15943
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4% isopropanol, 0.1M zinc acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jul 11, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 14655 / Num. obs: 14618 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MAR345data collection
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.057 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27869 734 5 %RANDOM
Rwork0.20103 ---
obs0.20475 13859 99.9 %-
all-25655 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.824 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20.68 Å20 Å2
2--1.35 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 19 168 2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222392
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9583248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90624.957117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70915403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8761515
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211833
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4291.51486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8422420
X-RAY DIFFRACTIONr_scbond_it1.3983906
X-RAY DIFFRACTIONr_scangle_it2.4454.5828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 59 -
Rwork0.289 979 -
obs--99.14 %
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)
13.6525-0.4022.67654.195-1.3447.751-0.0569-0.17630.32860.0467-0.1347-0.2298-0.593-0.00940.19160.12940.0347-0.00760.2626-0.03640.203878.6838-9.811364.1965
22.2875-0.39990.38551.9037-1.1813.2987-0.0358-0.08160.0370.0494-0.0367-0.0294-0.11810.00350.07250.23880.1363-0.02010.08910.00710.138263.805-4.556722.5231
31.35970.6657-0.77989.3413-2.56253.3825-0.07710.0869-0.0447-0.47540.29580.70510.27-0.3167-0.21870.19330.108-0.11070.1664-0.00150.158751.7232-32.234715.6263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A438 - 536
2X-RAY DIFFRACTION2A537 - 646
3X-RAY DIFFRACTION3A647 - 748

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