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- PDB-3ubg: Crystal structure of Drosophila N-cadherin EC1-3, II -

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Basic information

Entry
Database: PDB / ID: 3ubg
TitleCrystal structure of Drosophila N-cadherin EC1-3, II
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 / MOLECULAR REPLACEMENT / Resolution: 2.502 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 1.5Feb 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _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

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Assembly

Deposited unit
A: Neural-cadherin
B: Neural-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1689
Polymers71,8622
Non-polymers3067
Water7,134396
1
A: Neural-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1175
Polymers35,9311
Non-polymers1864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neural-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0514
Polymers35,9311
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-58 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.218, 113.769, 87.872
Angle α, β, γ (deg.)90.00, 123.57, 90.00
Int Tables number5
Space group name H-MC121
Detailsmonomer

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Components

#1: Protein Neural-cadherin / Cadherin-N / dN-cadherin


Mass: 35931.059 Da / Num. of mol.: 2 / Fragment: unp residues 434-753
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CadN, CG7100 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / References: UniProt: O15943
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 34% PEG 3350, 0.1M lithium sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9191 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 21, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 30083 / Num. obs: 30014 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rsym value: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.321 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→19.973 Å / SU ML: 0.91 / σ(F): 1.34 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1519 5.08 %RANDOM
Rwork0.1958 ---
all0.2226 30014 --
obs0.1992 29928 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.565 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.6763 Å20 Å2-3.6526 Å2
2--13.7356 Å2-0 Å2
3----5.0592 Å2
Refinement stepCycle: LAST / Resolution: 2.502→19.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 0 7 396 5314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085029
X-RAY DIFFRACTIONf_angle_d1.0836821
X-RAY DIFFRACTIONf_dihedral_angle_d15.2981909
X-RAY DIFFRACTIONf_chiral_restr0.069753
X-RAY DIFFRACTIONf_plane_restr0.004905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.502-2.58260.37811400.30852545X-RAY DIFFRACTION98
2.5826-2.67470.37971480.28152555X-RAY DIFFRACTION100
2.6747-2.78150.34261280.2592574X-RAY DIFFRACTION100
2.7815-2.90770.33131540.2322577X-RAY DIFFRACTION100
2.9077-3.06050.3141380.20182568X-RAY DIFFRACTION100
3.0605-3.25150.27721230.19192603X-RAY DIFFRACTION100
3.2515-3.50130.25461390.18812576X-RAY DIFFRACTION100
3.5013-3.85140.27841370.19362591X-RAY DIFFRACTION100
3.8514-4.40350.23271280.16752598X-RAY DIFFRACTION100
4.4035-5.52840.20371390.15012606X-RAY DIFFRACTION100
5.5284-19.97330.23231450.20172616X-RAY DIFFRACTION99

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