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- PDB-2omw: Crystal structure of InlA S192N Y369S/mEC1 complex -

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Basic information

Entry
Database: PDB / ID: 2omw
TitleCrystal structure of InlA S192N Y369S/mEC1 complex
Components
  • Epithelial-cadherin
  • Internalin-A
KeywordsCELL INVASION/CELL ADHESION / leucine-rich-repeat / invasion protein / IG-like domain / adhesion protein / CELL INVASION-CELL ADHESION COMPLEX
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 / Adherens junctions interactions / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / lateral loop ...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 / Adherens junctions interactions / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / lateral loop / positive regulation of cell-cell adhesion / desmosome / protein metabolic process / negative regulation of axon extension / regulation of protein localization to cell surface / cell-cell adhesion mediated by cadherin / trophectodermal cell differentiation / regulation of neuron migration / epithelial cell morphogenesis / alpha-catenin binding / bicellular tight junction assembly / Schmidt-Lanterman incisure / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / flotillin complex / intestinal epithelial cell development / node of Ranvier / catenin complex / cell-cell junction assembly / adherens junction organization / negative regulation of protein processing / apical junction complex / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / decidualization / establishment of skin barrier / negative regulation of protein localization to plasma membrane / canonical Wnt signaling pathway / axon terminus / synapse assembly / cytoskeletal protein binding / embryo implantation / protein tyrosine kinase binding / InlA-mediated entry of Listeria monocytogenes into host cells / peptidoglycan-based cell wall / protein localization to plasma membrane / cell periphery / cellular response to amino acid stimulus / adherens junction / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / beta-catenin binding / cell-cell adhesion / negative regulation of epithelial cell proliferation / cell-cell junction / cell migration / apical part of cell / regulation of protein localization / actin cytoskeleton organization / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding / in utero embryonic development / postsynapse / molecular adaptor activity / endosome / cadherin binding / protein domain specific binding / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / cell surface / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Immunoglobulin-like - #1220 / : ...: / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Immunoglobulin-like - #1220 / : / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Copper resistance protein CopC/internalin, immunoglobulin-like / Catenin binding domain superfamily / Cadherins / Cadherin / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cadherin-1 / Internalin A / Internalin A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWollert, T. / Heinz, D.W. / Schubert, W.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Extending the host range of Listeria monocytogenes by rational protein design.
Authors: Wollert, T. / Pasche, B. / Rochon, M. / Deppenmeier, S. / van den Heuvel, J. / Gruber, A.D. / Heinz, D.W. / Lengeling, A. / Schubert, W.D.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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: Internalin-A
B: Epithelial-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5097
Polymers61,3322
Non-polymers1775
Water15,889882
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-56 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.510, 112.281, 55.941
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Internalin-A


Mass: 49778.609 Da / Num. of mol.: 1 / Fragment: internalin domain / Mutation: S192N Y369S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: inlA / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25146, UniProt: P0DJM0*PLUS
#2: Protein Epithelial-cadherin


Mass: 11553.102 Da / Num. of mol.: 1 / Fragment: N-terminal domain of murine E-cadherin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6J / Gene: Cdh1 / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P09803
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 6000, LiCl, Na-Citrate, pH 5.2, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 53338 / % possible obs: 94.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.922.20.327185.1
1.92-1.992.60.252189.9
1.99-2.082.20.182188.1
2.08-2.192.30.15191.8
2.19-2.332.50.135194.3
2.33-2.512.50.119196.8
2.51-2.762.50.11198.3
2.76-3.162.80.08199.7
3.16-3.992.80.05199.9
3.99-502.80.035199.7

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Phasing

Phasing MRRfactor: 0.32 / Cor.coef. Fo:Fc: 0.736
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O6S

1o6s


Resolution: 1.85→110.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.885 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20744 2728 5.1 %RANDOM
Rwork0.1647 ---
obs0.16696 50581 93.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.24 Å2
2--0.89 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.85→110.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 5 882 5196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224908
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9696808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.86227.65217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96215872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4491511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023801
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1760.22467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2850.23393
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2764
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2520.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.10323280
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70335258
X-RAY DIFFRACTIONr_scbond_it2.621828
X-RAY DIFFRACTIONr_scangle_it3.65931531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.855→1.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 171 -
Rwork0.223 3110 -
obs--78.42 %

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