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- PDB-2qvf: mouse E-cadherin domains 1,2 -

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Basic information

Entry
Database: PDB / ID: 2qvf
Titlemouse E-cadherin domains 1,2
ComponentsEpithelial-cadherin (E-cadherin) (Uvomorulin) (Cadherin-1) (ARC-1) (CD324 antigen)
KeywordsCELL ADHESION / Cadherin / Ecad / E-cadherin / strand swap / Calcium / Cell junction / Cleavage on pair of basic residues / Glycoprotein / Membrane / Phosphorylation / 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 / Schmidt-Lanterman incisure / cellular response to indole-3-methanol / flotillin complex / 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 localization to plasma membrane / negative regulation of protein processing / 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 / negative regulation of canonical Wnt signaling pathway / trans-Golgi network / cell morphogenesis / 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: 2.4 Å
AuthorsCarroll, K.J.
CitationJournal: To be Published
Title: E-cadherin domains 1,2
Authors: Carroll, K.J.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
B: Epithelial-cadherin (E-cadherin) (Uvomorulin) (Cadherin-1) (ARC-1) (CD324 antigen)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4215
Polymers23,2611
Non-polymers1604
Water3,045169
1
B: Epithelial-cadherin (E-cadherin) (Uvomorulin) (Cadherin-1) (ARC-1) (CD324 antigen)
hetero molecules

B: Epithelial-cadherin (E-cadherin) (Uvomorulin) (Cadherin-1) (ARC-1) (CD324 antigen)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,84210
Polymers46,5222
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.711, 42.669, 58.132
Angle α, β, γ (deg.)90.000, 111.970, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer based on a Trp2 strand swap into the hydrophobic pocket of a dimer mate. 1 mol/ASU.

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Components

#1: Protein Epithelial-cadherin (E-cadherin) (Uvomorulin) (Cadherin-1) (ARC-1) (CD324 antigen)


Mass: 23260.865 Da / Num. of mol.: 1 / Fragment: Cadherin 1, Cadherin 2, UNP residues 157-369 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P09803
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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: 3.33 Å3/Da / Density % sol: 63.07 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 12255 / % possible obs: 95.44 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1P

1q1p


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.867 / SU B: 9.169 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 551 4.7 %RANDOM
Rwork0.23 ---
obs0.232 11732 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å2-0.11 Å2
2--1.33 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 4 169 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221667
X-RAY DIFFRACTIONr_angle_refined_deg0.8851.9632276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1775212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56726.08174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88415274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.387156
X-RAY DIFFRACTIONr_chiral_restr0.0520.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021268
X-RAY DIFFRACTIONr_nbd_refined0.1550.2650
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.225
X-RAY DIFFRACTIONr_mcbond_it0.1911.51094
X-RAY DIFFRACTIONr_mcangle_it0.33921744
X-RAY DIFFRACTIONr_scbond_it0.3633643
X-RAY DIFFRACTIONr_scangle_it0.664.5532
LS refinement shellResolution: 2.4→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 28 -
Rwork0.306 585 -
obs-613 68.19 %

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