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

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Basic information

Entry
Database: PDB / ID: 2omt
TitleCrystal structure of InlA G194S+S/hEC1 complex
Components
  • Epithelial-cadherin; E-Cad/CTF1
  • 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
Class 1 internalin InlA / Cadherin-1 / Internalin A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 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; E-Cad/CTF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5434
Polymers61,4682
Non-polymers762
Water10,773598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.240, 88.470, 110.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Internalin-A


Mass: 49944.785 Da / Num. of mol.: 1 / Fragment: internalin domain / Mutation: 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: A4GWM6*PLUS
#2: Protein Epithelial-cadherin; E-Cad/CTF1


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.: 598 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
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: 2→40 Å / Num. obs: 36174 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 23.269 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.44
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.9 / Num. measured obs: 19611 / Num. unique all: 4620 / % possible all: 91.5

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Phasing

Phasing MRRfactor: 0.535 / Cor.coef. Fo:Fc: 0.467
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O6S

1o6s


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.871 / SU B: 6.878 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1800 5 %RANDOM
Rwork0.194 ---
obs0.199 36029 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.242 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--0.77 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 2 598 4910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224610
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.9776339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7855615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.23627.263190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7615814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.231511
X-RAY DIFFRACTIONr_chiral_restr0.140.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023448
X-RAY DIFFRACTIONr_nbd_refined0.2420.22442
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2522
X-RAY DIFFRACTIONr_metal_ion_refined0.2820.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.246
X-RAY DIFFRACTIONr_mcbond_it1.1091.53074
X-RAY DIFFRACTIONr_mcangle_it1.68624905
X-RAY DIFFRACTIONr_scbond_it2.99431732
X-RAY DIFFRACTIONr_scangle_it4.1654.51430
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 114 -
Rwork0.247 2515 -
obs-2629 96.23 %

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