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- PDB-2omu: Crystal structure of InlA G194S+S Y369S/hEC1 complex -

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Basic information

Entry
Database: PDB / ID: 2omu
TitleCrystal structure of InlA G194S+S Y369S/hEC1 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


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 / cell wall / 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 / 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 / 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: 1.8 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: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4674
Polymers61,3922
Non-polymers762
Water13,962775
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.010, 54.273, 68.643
Angle α, β, γ (deg.)74.98, 80.82, 67.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Internalin-A


Mass: 49868.691 Da / Num. of mol.: 1 / Fragment: internalin domain / Mutation: G194S+S 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: G2K3G6*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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
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: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 50001 / % possible obs: 93.7 % / Rmerge(I) obs: 0.094 / Χ2: 0.754 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.860.62339600.951174.9
1.86-1.940.4645570.966185.1
1.94-2.030.34348240.969190.5
2.03-2.130.24750420.943194.3
2.13-2.270.22951800.89197.1
2.27-2.440.17352630.813198.3
2.44-2.690.14852550.788198.7
2.69-3.070.152780.705199
3.07-3.870.0553160.491199.3
3.87-200.0353260.332199.7

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å20.02 Å
Translation1.8 Å20.02 Å

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Processing

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

1o6s


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.861 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2548 5.1 %RANDOM
Rwork0.164 ---
obs0.167 49998 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.77 Å2-0.06 Å2
2---0.75 Å2-0.16 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 2 775 5093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224808
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9746661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.41627.536207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53515871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9851511
X-RAY DIFFRACTIONr_chiral_restr0.120.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023644
X-RAY DIFFRACTIONr_nbd_refined0.1820.22438
X-RAY DIFFRACTIONr_nbtor_refined0.2790.23244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2702
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.239
X-RAY DIFFRACTIONr_mcbond_it1.64723231
X-RAY DIFFRACTIONr_mcangle_it2.17835120
X-RAY DIFFRACTIONr_scbond_it1.91821815
X-RAY DIFFRACTIONr_scangle_it2.7631503
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 144 -
Rwork0.288 2593 -
obs-2737 70.98 %
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)
14.3498-0.12567.5870.0792-0.592715.0801-0.51120.4667-0.06380.1194-0.04080.2555-0.1888-0.21610.55200.0004-0.00020.0001-0.0001-0.0002-8.996-3.275-32.26
20.26150.07060.07190.84280.20370.0610.01040.02230.0103-0.1686-0.0066-0.0903-0.04270.0175-0.00380.02360.0020.0428-0.02080.0149-0.045717.2654.8240.38
30.3541-0.4835-0.31621.1496-0.61312.5681-0.1676-0.08070.03660.31830.1183-0.033-0.2911-0.03720.04930.05990.0628-0.01980.0042-0.0216-0.03879.3163930.904
41.6508-0.1343-0.00361.43110.99032.61460.0518-0.08880.1819-0.1474-0.15980.16030.078-0.0090.108-0.0363-0.0030.0034-0.06830.0018-0.01517.72913.12-0.928
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA36 - 781 - 43
22AA79 - 41544 - 380
33AA416 - 497381 - 462
44BB1 - 1005 - 104

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