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- PDB-1o6s: Internalin (Listeria monocytogenes) / E-Cadherin (human) Recognit... -

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Basic information

Entry
Database: PDB / ID: 1o6s
TitleInternalin (Listeria monocytogenes) / E-Cadherin (human) Recognition Complex
Components
  • E-CADHERIN
  • INTERNALIN A
KeywordsBACTERIAL INFECTION / LEUCINE RICH REPEAT / CELL ADHESION / CELL-WALL SURFACE PROTEIN
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 ...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 / flotillin complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / adherens junction organization / Formation of definitive endoderm / catenin complex / Apoptotic cleavage of cell adhesion proteins / cell-cell junction assembly / Adherens junctions interactions / GTPase activating protein binding / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / apical junction complex / homophilic cell-cell adhesion / 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 / peptidoglycan-based cell wall / negative regulation of cell migration / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell-cell adhesion / beta-catenin binding / positive regulation of protein import into nucleus / response to toxic substance / cytoplasmic side of plasma membrane / cell morphogenesis / 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 / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / 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
AuthorsSchubert, W.-D. / Urbanke, C. / Ziehm, T. / Beier, V. / Machner, M.P. / Domann, E. / Wehland, J. / Chakraborty, T. / Heinz, D.W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure of Internalin, a Major Invasion Protein of Listeria Monocytogenes, in Complex with its Human Receptor E-Cadherin
Authors: Schubert, W.-D. / Urbanke, C. / Ziehm, T. / Beier, V. / Machner, M.P. / Domann, E. / Wehland, J. / Chakraborty, T. / Heinz, D.W.
History
DepositionOct 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERNALIN A
B: E-CADHERIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9497
Polymers61,7622
Non-polymers1875
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.378, 86.859, 110.723
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: 50239.133 Da / Num. of mol.: 1 / Fragment: FUNCTIONAL DOMAIN, RESIDUES 36-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Variant: SEROVAR 1/2A / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25146, UniProt: P0DJM0*PLUS
#2: Protein E-CADHERIN


Mass: 11523.009 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 156-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P12830
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST FIVE RESIDUES (GPLGS) INTRODUCED THROUGH CLONING PROCEDURE

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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: 2.14 Å3/Da / Density % sol: 42 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: VAPOUR DIFFUSION / HANGING DROP 10 MG/ML IN 10 MM HEPES PH 7.0, 26% PEG 4000, 100 MM MES/TRIS PH 7.0, 100 MM SODIUM ACETATE, 50 MM CACL2
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
226 %PEG40001reservoir
30.1 MMES-Tris1reservoirpH7.0
4100 mMsodium acetate1reservoir
550 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.8→25.1 Å / Num. obs: 50336 / % possible obs: 92 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.4 / % possible all: 84.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25 Å / Num. obs: 46306
Reflection shell
*PLUS
% possible obs: 84.3 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→69.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.368 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2344 5.1 %RANDOM
Rwork0.168 ---
obs0.171 43962 92.1 %-
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: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4301 0 5 537 4843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214681
X-RAY DIFFRACTIONr_bond_other_d0.0030.024210
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9656437
X-RAY DIFFRACTIONr_angle_other_deg0.91739926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9125629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025333
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02771
X-RAY DIFFRACTIONr_nbd_refined0.2120.2900
X-RAY DIFFRACTIONr_nbd_other0.2460.25259
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8961.53034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55424999
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3631647
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8794.51438
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 156
Rwork0.278 2951
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 69 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.78

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