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- PDB-3lnf: Crystal structure of E-cadherin EC12 K14EW2A -

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Basic information

Entry
Database: PDB / ID: 3lnf
TitleCrystal structure of E-cadherin EC12 K14EW2A
ComponentsCadherin-1
KeywordsCELL ADHESION / cadherin / Calcium / Cell junction / Cell membrane / Glycoprotein / Transmembrane
Function / homology
Function and homology information


uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / Adherens junctions interactions / Degradation of the extracellular matrix / regulation of neuron migration / Integrin cell surface interactions ...uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / Adherens junctions interactions / Degradation of the extracellular matrix / regulation of neuron migration / Integrin cell surface interactions / positive regulation of cell-cell adhesion / lateral loop / gamma-catenin binding / cell-cell adhesion mediated by cadherin / negative regulation of axon extension / regulation of protein localization to cell surface / trophectodermal cell differentiation / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / Schmidt-Lanterman incisure / epithelial cell morphogenesis / bicellular tight junction assembly / intestinal epithelial cell development / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / node of Ranvier / protein metabolic process / catenin complex / cell-cell junction assembly / negative regulation of protein processing / negative regulation of protein localization to plasma membrane / GTPase activating protein binding / adherens junction organization / apical junction complex / ankyrin binding / cochlea development / negative regulation of cell-cell adhesion / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / decidualization / canonical Wnt signaling pathway / lateral plasma membrane / establishment of skin barrier / axon terminus / embryo implantation / synapse assembly / protein tyrosine kinase binding / cytoskeletal protein binding / cell adhesion molecule binding / negative regulation of cell migration / cell periphery / protein localization to plasma membrane / cellular response to amino acid stimulus / sensory perception of sound / adherens junction / cell morphogenesis / trans-Golgi network / negative regulation of canonical Wnt signaling pathway / cytoplasmic side of plasma membrane / cell-cell adhesion / beta-catenin binding / positive regulation of protein import into nucleus / regulation of protein localization / negative regulation of epithelial cell proliferation / cell-cell junction / actin cytoskeleton / apical part of cell / lamellipodium / cell junction / actin cytoskeleton organization / postsynapse / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding / in utero embryonic development / molecular adaptor activity / endosome / cadherin binding / axon / protein domain specific binding / glutamatergic synapse / calcium ion binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain 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 / 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: 2.5 Å
AuthorsJin, X. / Harrison, O. / Shapiro, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Two-step adhesive binding by classical cadherins.
Authors: Harrison, O.J. / Bahna, F. / Katsamba, P.S. / Jin, X. / Brasch, J. / Vendome, J. / Ahlsen, G. / Carroll, K.J. / Price, S.R. / Honig, B. / Shapiro, L.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-1
B: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5328
Polymers46,2912
Non-polymers2406
Water3,045169
1
A: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2664
Polymers23,1461
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2664
Polymers23,1461
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.107, 47.383, 69.897
Angle α, β, γ (deg.)70.58, 88.13, 75.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cadherin-1 / / Epithelial cadherin / E-cadherin / Uvomorulin / ARC-1 / E-Cad/CTF1 / E-Cad/CTF2 / E-Cad/CTF3


Mass: 23145.668 Da / Num. of mol.: 2 / Fragment: UNP residues 157-369 / Mutation: K14E,W2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09803
#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 / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2M ammonium sulfate, 0.1M Tris-Cl pH 8.5, 15% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97897 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17934 / Num. obs: 17683 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDH

1edh


Resolution: 2.5→28.635 Å / SU ML: 0.36 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 902 5.14 %random
Rwork0.1842 ---
obs0.1872 17538 96.07 %-
all-17683 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.401 Å2 / ksol: 0.369 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→28.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 6 169 3351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113233
X-RAY DIFFRACTIONf_angle_d1.3374413
X-RAY DIFFRACTIONf_dihedral_angle_d19.4771174
X-RAY DIFFRACTIONf_chiral_restr0.069522
X-RAY DIFFRACTIONf_plane_restr0.007583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4987-2.65510.31771400.24482464X-RAY DIFFRACTION86
2.6551-2.860.30121330.22122816X-RAY DIFFRACTION97
2.86-3.14740.25381540.19362851X-RAY DIFFRACTION97
3.1474-3.60210.26291570.16442795X-RAY DIFFRACTION98
3.6021-4.53540.17791650.15162847X-RAY DIFFRACTION99
4.5354-28.63650.2211530.16322863X-RAY DIFFRACTION99

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