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- PDB-3qrb: crystal structure of E-cadherin EC1-2 P5A P6A -

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Basic information

Entry
Database: PDB / ID: 3qrb
Titlecrystal structure of E-cadherin EC1-2 P5A P6A
ComponentsCadherin-1
KeywordsCELL ADHESION / cadherin
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 / positive regulation of cell-cell adhesion / 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 / positive regulation of cell-cell adhesion / Integrin cell surface interactions / lateral loop / regulation of neuron migration / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / regulation of protein localization to cell surface / trophectodermal cell differentiation / alpha-catenin binding / epithelial cell morphogenesis / flotillin complex / Schmidt-Lanterman incisure / bicellular tight junction assembly / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / intestinal epithelial cell development / node of Ranvier / protein metabolic process / catenin complex / negative regulation of protein processing / cell-cell junction assembly / negative regulation of protein localization to plasma membrane / adherens junction organization / apical junction complex / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / decidualization / canonical Wnt signaling pathway / establishment of skin barrier / axon terminus / synapse assembly / cytoskeletal protein binding / embryo implantation / protein tyrosine kinase binding / cell periphery / protein localization to plasma membrane / adherens junction / sensory perception of sound / cellular response to amino acid stimulus / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / beta-catenin binding / cell-cell adhesion / negative regulation of epithelial cell proliferation / regulation of protein localization / cell-cell junction / apical part of cell / actin cytoskeleton organization / postsynapse / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding / in utero embryonic development / molecular adaptor activity / endosome / cadherin binding / protein domain specific binding / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / cell surface / 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
TRIETHYLENE GLYCOL / Cadherin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJin, X. / Shapiro, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Molecular design principles underlying beta-strand swapping in the adhesive dimerization of cadherins.
Authors: Vendome, J. / Posy, S. / Jin, X. / Bahna, F. / Ahlsen, G. / Shapiro, L. / Honig, B.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Sep 13, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,20714
Polymers46,4182
Non-polymers78912
Water16,268903
1
A: Cadherin-1
hetero molecules

A: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,20714
Polymers46,4182
Non-polymers78912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2680 Å2
ΔGint-34 kcal/mol
Surface area22250 Å2
MethodPISA
2
B: Cadherin-1
hetero molecules

B: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,20714
Polymers46,4182
Non-polymers78912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3560 Å2
ΔGint-27 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.185, 92.583, 79.465
Angle α, β, γ (deg.)90.00, 92.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

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Components

#1: Protein Cadherin-1 / ARC-1 / Epithelial cadherin / E-cadherin / Uvomorulin


Mass: 23208.793 Da / Num. of mol.: 2
Fragment: Cadherin 1 and Cadherin 2 Domains, UNP residues 157-369
Mutation: P161A, P162A
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 903 / 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: 4.4 Å3/Da / Density % sol: 72.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG8000, 10% ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 74512 / Num. obs: 73693 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF5

1ff5


Resolution: 1.8→44.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.567 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17805 3712 5 %RANDOM
Rwork0.16162 ---
obs0.16246 69888 98.81 %-
all-73693 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.787 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.39 Å2
2--0.36 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 42 903 4209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223434
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9644691
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97126.154156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48415568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2311513
X-RAY DIFFRACTIONr_chiral_restr0.090.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212609
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21553
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22336
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2692
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.226
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.264
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5961.52168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14623559
X-RAY DIFFRACTIONr_scbond_it2.0231266
X-RAY DIFFRACTIONr_scangle_it3.4924.51118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 273 -
Rwork0.294 5003 -
obs--96.7 %
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)
12.0777-1.2810.35032.5836-0.72012.1974-0.00380.07490.0113-0.0617-0.0393-0.04010.04310.08580.04310.002700.00250.0091-0.00410.009957.6307-14.137730.5549
25.3979-3.01570.70842.1164-0.50240.36570.20220.28130.0861-0.1289-0.1966-0.0490.0046-0.0127-0.00570.07050.0660.00850.0816-0.00910.039922.802315.377720.7301
31.76181.4452-0.33252.5363-0.66192.15390.0175-0.06620.0167-0.0123-0.0532-0.0726-0.14090.26410.03560.0116-0.02040.00250.0404-0.00680.016361.15756.88887.9874
45.85623.8249-0.192.6265-0.16660.52920.4025-0.4529-0.29190.2485-0.321-0.14590.217-0.1439-0.08150.1413-0.1168-0.04630.11210.02380.053828.7394-24.853517.1608
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 97
2X-RAY DIFFRACTION2A98 - 213
3X-RAY DIFFRACTION3B1 - 97
4X-RAY DIFFRACTION4B98 - 213

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