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- PDB-1q1p: E-Cadherin activation -

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Basic information

Entry
Database: PDB / ID: 1q1p
TitleE-Cadherin activation
ComponentsEpithelial-cadherin
KeywordsCELL ADHESION
Function / homology
Function and homology information


uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / desmosome assembly / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / Adherens junctions interactions / Degradation of the extracellular matrix / RHO GTPases activate IQGAPs / Degradation of CDH1 ...uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / desmosome assembly / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / Adherens junctions interactions / Degradation of the extracellular matrix / RHO GTPases activate IQGAPs / Degradation of CDH1 / Integrin cell surface interactions / Regulation of CDH1 Function / gamma-catenin binding / desmosome / positive regulation of cell-cell adhesion / lateral loop / regulation of protein localization to cell surface / negative regulation of axon extension / cell-cell adhesion mediator activity / alpha-catenin binding / cellular response to indole-3-methanol / trophectodermal cell differentiation / calcium-dependent cell-cell adhesion / bicellular tight junction assembly / intestinal epithelial cell development / flotillin complex / Schmidt-Lanterman incisure / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / epithelial cell morphogenesis / adherens junction organization / catenin complex / regulation of neuron migration / node of Ranvier / cell-cell junction assembly / negative regulation of protein processing / GTPase activating protein binding / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / apical junction complex / homophilic cell-cell adhesion / decidualization / microvillus / establishment of skin barrier / cochlea development / lateral plasma membrane / negative regulation of protein localization to plasma membrane / positive regulation of protein localization / cytoskeletal protein binding / synapse assembly / embryo implantation / cell adhesion molecule binding / axon terminus / protein tyrosine kinase binding / negative regulation of cell migration / cell periphery / protein localization to plasma membrane / adherens junction / cellular response to amino acid stimulus / trans-Golgi network / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / cell-cell adhesion / positive regulation of protein import into nucleus / beta-catenin binding / cytoplasmic side of plasma membrane / cell morphogenesis / negative regulation of epithelial cell proliferation / apical part of cell / cell-cell junction / cell junction / regulation of protein localization / cell migration / lamellipodium / actin cytoskeleton / regulation of gene expression / actin cytoskeleton organization / protein phosphatase binding / molecular adaptor activity / in utero embryonic development / basolateral plasma membrane / endosome / postsynapse / cadherin binding / protein domain specific binding / axon / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / 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 / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHaussinger, D. / Stetefeld, J.
CitationJournal: Embo J. / Year: 2004
Title: Proteolytic E-cadherin activation followed by solution NMR and X-ray crystallography.
Authors: Haussinger, D. / Ahrens, T. / Aberle, T. / Engel, J. / Stetefeld, J. / Grzesiek, S.
History
DepositionJul 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2012Group: Derived calculations
Revision 1.4Aug 16, 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_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_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: Epithelial-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2664
Polymers23,1461
Non-polymers1203
Water4,197233
1


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

A: Epithelial-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5328
Polymers46,2922
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1710 Å2
ΔGint-39 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.204, 48.601, 58.669
Angle α, β, γ (deg.)90.00, 113.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23145.777 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.16 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.18→37.47 Å / Num. all: 5632 / Num. obs: 5324 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.131 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FF5.pdb

1ff5


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.774 / SU B: 32.728 / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.625 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30484 256 4.6 %RANDOM
Rwork0.25867 ---
obs0.26155 5324 100 %-
all-5632 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-2.22 Å2
2---2.01 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 3 233 1864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221659
X-RAY DIFFRACTIONr_bond_other_d0.0030.021480
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9542264
X-RAY DIFFRACTIONr_angle_other_deg1.51433469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7753211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.415291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1580.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021854
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02294
X-RAY DIFFRACTIONr_nbd_refined0.3320.3540
X-RAY DIFFRACTIONr_nbd_other0.3010.31904
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.5168
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2210.511
X-RAY DIFFRACTIONr_metal_ion_refined0.2790.54
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4960.54
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1780.51
X-RAY DIFFRACTIONr_mcbond_it1.1341.51060
X-RAY DIFFRACTIONr_mcangle_it2.00221735
X-RAY DIFFRACTIONr_scbond_it2.6943599
X-RAY DIFFRACTIONr_scangle_it4.5014.5529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 21
Rwork0.298 388
Refinement TLS params.Method: refined / Origin x: -1.3919 Å / Origin y: 0.6416 Å / Origin z: 26.0387 Å
111213212223313233
T0.0421 Å20.0315 Å2-0.0525 Å2-0.1243 Å2-0.0127 Å2--0.0725 Å2
L0.2895 °20.6424 °20.7992 °2-0.7144 °20.7913 °2--1.2331 °2
S-0.1488 Å °0.1687 Å °0.0951 Å °-0.1267 Å °-0.0082 Å °0.0784 Å °-0.1232 Å °0.1076 Å °0.157 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 111 - 10
2X-RAY DIFFRACTION1AA12 - 1911 - 18
3X-RAY DIFFRACTION1AA20 - 2619 - 25
4X-RAY DIFFRACTION1AA35 - 9834 - 97
5X-RAY DIFFRACTION1AA99 - 10798 - 106
6X-RAY DIFFRACTION1AA108 - 213107 - 212

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