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- PDB-2omx: Crystal structure of InlA S192N G194S+S/hEC1 complex -

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Basic information

Entry
Database: PDB / ID: 2omx
TitleCrystal structure of InlA S192N G194S+S/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 heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / flotillin complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / Formation of definitive endoderm / catenin complex / Apoptotic cleavage of cell adhesion proteins / adherens junction organization / GTPase activating protein binding / cell-cell junction assembly / Adherens junctions interactions / ankyrin binding / negative regulation of cell-cell adhesion / apical junction complex / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / Integrin cell surface interactions / RHO GTPases activate IQGAPs / synapse assembly / cell adhesion molecule binding / positive regulation of protein localization / Degradation of the extracellular matrix / Transcriptional and post-translational regulation of MITF-M expression and activity / InlA-mediated entry of Listeria monocytogenes into host cells / protein tyrosine kinase binding / negative regulation of cell migration / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell morphogenesis / beta-catenin binding / cell-cell adhesion / cytoplasmic side of plasma membrane / positive regulation of protein import into nucleus / response to toxic substance / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell junction / cell migration / lamellipodium / actin cytoskeleton / regulation of gene expression / postsynapse / endosome / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / extracellular region / identical protein binding / membrane / 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 / Cadherin / Catenin binding domain superfamily / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Cadherins / 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
InlA / Cadherin-1 / Internalin A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _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)61,9144
Polymers61,8382
Non-polymers762
Water12,737707
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.887, 54.160, 68.811
Angle α, β, γ (deg.)74.75, 80.69, 67.71
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Internalin-A


Mass: 49971.805 Da / Num. of mol.: 1 / Fragment: internalin domain / Mutation: S192N G194S+S
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: A4GWL5*PLUS
#2: Protein Epithelial-cadherin


Mass: 11866.303 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
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: X11 / 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: 1.65→20 Å / Num. obs: 62497 / % possible obs: 90.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.710.715164.1
1.71-1.780.688177.2
1.78-1.860.624188.2
1.86-1.960.393192.7
1.96-2.080.235195
2.08-2.240.175195.7
2.24-2.460.135197.3
2.46-2.820.103198.6
2.82-3.550.057199
3.55-200.036199.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.65 Å20.05 Å
Translation1.65 Å20.05 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: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.348 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22323 3001 5.1 %RANDOM
Rwork0.16687 ---
obs0.16973 56061 92.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å21.19 Å2-0.72 Å2
2--0 Å2-0.16 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 2 707 5053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.9676858
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.06927.679224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80815882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5071510
X-RAY DIFFRACTIONr_chiral_restr0.1490.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023785
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.22520
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23403
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2592
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.423268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04135234
X-RAY DIFFRACTIONr_scbond_it2.93421882
X-RAY DIFFRACTIONr_scangle_it4.09631570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 167 -
Rwork0.259 3245 -
obs--72.41 %
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)
16.7422-1.52429.23880.70440.520831.5864-0.40130.56550.11090.3374-0.19460.203-0.1597-0.29710.5959-0.0002-0.00010.0017-0.0005-0.00050.0001-11.248-3.021-33.338
20.31820.0120.13421.07270.26080.23180.04210.03350.0281-0.2031-0.0331-0.1188-0.03480.0126-0.0090.0465-0.01180.0937-0.0880.0074-0.071514.7525.402-0.339
30.3763-0.4413-0.29091.0059-0.52342.6077-0.2365-0.17860.05610.42070.1776-0.0132-0.3338-0.08340.05890.17070.08130.0237-0.0176-0.0402-0.05116.66939.70930.06
42.0476-0.4983-0.36132.4650.89932.94480.0865-0.05350.2398-0.197-0.1140.23680.14560.02570.02750.0148-0.02260.0607-0.13380.0061-0.01595.22713.686-1.916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA36 - 781 - 43
2X-RAY DIFFRACTION2AA79 - 41544 - 380
3X-RAY DIFFRACTION3AA416 - 497381 - 462
4X-RAY DIFFRACTION4BB1 - 1005 - 104

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