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- PDB-2omz: Crystal structure of InlA Y369A/hEC1 complex -

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Basic information

Entry
Database: PDB / ID: 2omz
TitleCrystal structure of InlA Y369A/hEC1 complex
Components
  • Epithelial-cadherin
  • Internalin-A
KeywordsCELL INVASION/CELL ADHESION / leucine-rich-repeat / nvasion protein / IG-like domain / adhesion protein / CELL INVASION-CELL ADHESION COMPLEX
Function / homology
Function and homology information


response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Formation of definitive endoderm ...response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Formation of definitive endoderm / Adherens junctions interactions / catenin complex / Apoptotic cleavage of cell adhesion proteins / GTPase activating protein binding / cell-cell junction assembly / adherens junction organization / apical junction complex / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / RHO GTPases activate IQGAPs / Integrin cell surface interactions / cell adhesion molecule binding / synapse assembly / InlA-mediated entry of Listeria monocytogenes into host cells / Degradation of the extracellular matrix / negative regulation of cell migration / peptidoglycan-based cell wall / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / cell morphogenesis / trans-Golgi network / cytoplasmic side of plasma membrane / response to toxic substance / beta-catenin binding / cell-cell adhesion / positive regulation of protein import into nucleus / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / actin cytoskeleton / lamellipodium / cell junction / postsynapse / regulation of gene expression / endosome / response to xenobiotic stimulus / cadherin binding / glutamatergic synapse / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
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 / Cadherin prodomain like ...: / 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 / Copper resistance protein CopC/internalin, immunoglobulin-like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Leucine rich repeat 4 / Cadherins / Leucine Rich repeats (2 copies) / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / 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
Internalin A / Cadherin-1 / Internalin A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWollert, T. / Heinz, D.W. / Schubert, W.D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Thermodynamically reengineering the listerial invasion complex InlA/E-cadherin.
Authors: Wollert, T. / Heinz, D.W. / Schubert, W.D.
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Data collection / Database references
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: Internalin-A
B: Epithelial-cadherin


Theoretical massNumber of molelcules
Total (without water)61,6562
Polymers61,6562
Non-polymers00
Water14,286793
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.323, 84.741, 108.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Internalin-A


Mass: 50133.012 Da / Num. of mol.: 1 / Fragment: internalin domain / Mutation: Y369A
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: 11523.009 Da / Num. of mol.: 1 / Fragment: N-terminal domain of human E-cadherin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH1, CDHE, UVO / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12830
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 67637 / % possible obs: 99.4 % / Rmerge(I) obs: 0.045 / Χ2: 1.094 / Net I/σ(I): 20.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.630.29232071.138195.3
1.63-1.660.25833081.139199.8
1.66-1.690.22933211.138198.9
1.69-1.720.19633701.138199.7
1.72-1.760.17733291.143199.5
1.76-1.80.14933571.128199.4
1.8-1.850.1233531.07199.6
1.85-1.90.1133691.1081100
1.9-1.950.10633341.143199.6
1.95-2.020.07133701.011199.9
2.02-2.090.07133961.061199.9
2.09-2.170.05433871.002199.9
2.17-2.270.0733641.149199.9
2.27-2.390.04534201.064199.9
2.39-2.540.0433941.0771100
2.54-2.740.03834241.0861100
2.74-3.010.03334151.151100
3.01-3.450.02834651.075199.9
3.45-4.340.02634991.04199.9
4.34-400.02235551.033197

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Phasing

Phasing MRRfactor: 0.595 / Cor.coef. Fo:Fc: 0.196
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.2phasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O6S

1o6s


Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.547 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3432 5.1 %RANDOM
Rwork0.153 ---
obs0.155 67548 99.38 %-
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: 11.235 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4323 0 0 793 5116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0214744
X-RAY DIFFRACTIONr_bond_other_d0.0190.024275
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9636545
X-RAY DIFFRACTIONr_angle_other_deg1.529310078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9285644
X-RAY DIFFRACTIONr_chiral_restr0.1330.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025453
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02789
X-RAY DIFFRACTIONr_nbd_refined0.1640.2760
X-RAY DIFFRACTIONr_nbd_other0.1640.24998
X-RAY DIFFRACTIONr_nbtor_other0.0660.22608
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.070.2640
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0870.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.2104
X-RAY DIFFRACTIONr_mcbond_it2.23923079
X-RAY DIFFRACTIONr_mcangle_it3.19835094
X-RAY DIFFRACTIONr_scbond_it3.36221665
X-RAY DIFFRACTIONr_scangle_it5.18431451
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.261 244
Rwork0.213 4534
obs-4778
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)
11.5685-0.76751.31.7093-0.53551.45960.1012-0.0364-0.1483-0.14270.06770.1360.1228-0.0869-0.16890.0653-0.0162-0.02650.05390.03030.065855.78840.59340.882
20.10240.0994-0.10610.00150.02490.1713-0.00210.00620.0356-0.01640.0310.0537-0.0078-0.0203-0.02880.03870.0105-0.00680.05460.02660.077558.0326.02780.436
30.37040.342-0.20871.5894-0.30610.20990.0717-0.0073-0.10640.1422-0.1063-0.03190.03740.00610.03450.0555-0.0198-0.02360.03120.01370.089623.1563.458101.744
41.64810.276-0.02960.7555-0.67671.0990.06260.1970.10690.04390.01240.0539-0.0036-0.0273-0.07490.0070.01390.00450.07260.04580.037945.34824.66775.163
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA32 - 781 - 47
22AA79 - 41448 - 383
33AA415 - 496384 - 465
44BB-3 - 1001 - 104

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