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- PDB-8h62: Crystal structure of Internalin A from Listeria monocytogenes wit... -

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Basic information

Entry
Database: PDB / ID: 8h62
TitleCrystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12
Components
  • Cadherin-1
  • Internalin A
KeywordsCELL INVASION / Internalin A Cadherin Bacterial invasion nanobody Surface plasmon resonance Isothermal titration calorimetry
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 / Cadherin prodomain like / Cadherin prodomain ...: / 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 / 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 / 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, 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
Similarity search - Domain/homology
ACETATE ION / Internalin A / Cadherin-1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCaaveiro, J.M.M. / Nagatoish, S. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H02420 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes.
Authors: Yamazaki, T. / Nagatoishi, S. / Yamawaki, T. / Nozawa, T. / Matsunaga, R. / Nakakido, M. / Caaveiro, J.M.M. / Nakagawa, I. / Tsumoto, K.
History
DepositionOct 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Internalin A
B: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2697
Polymers73,0492
Non-polymers2195
Water11,349630
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.350, 69.580, 72.490
Angle α, β, γ (deg.)101.480, 97.770, 105.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Internalin A


Mass: 49914.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: inlA, lmo0433, intlA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DJM0
#2: Protein Cadherin-1 / CAM 120/80 / Epithelial cadherin / E-cadherin / Uvomorulin / E-cadherin EC12


Mass: 23134.660 Da / Num. of mol.: 1 / Mutation: C163S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH1, CDHE, UVO / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P12830
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium acetate 45% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→34.8 Å / Num. obs: 71483 / % possible obs: 92.3 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.8
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4418 / CC1/2: 0.837 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.2.1data reduction
Aimless0.5.32data scaling
MOLREP2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o6s 4zmt

1o6s

4zmt


Resolution: 1.91→34.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.527 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 2835 4 %RANDOM
Rwork0.1763 ---
obs0.1776 68640 92.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.26 Å2 / Biso mean: 26.343 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20.41 Å2-0.36 Å2
2--1.79 Å20.55 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 1.91→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 8 633 5777
Biso mean--40.61 34.12 -
Num. residues----675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125255
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164828
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6397201
X-RAY DIFFRACTIONr_angle_other_deg0.4581.54811320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5055685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.258510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30710897
X-RAY DIFFRACTIONr_chiral_restr0.0630.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
LS refinement shellResolution: 1.91→1.959 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 209 -
Rwork0.289 5045 -
all-5254 -
obs--92.22 %
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)
10.7059-0.1478-0.12830.58180.20420.5639-0.0086-0.0822-0.0410.02090.0041-0.03180.06350.00610.00450.0080.00660.00250.06250.02360.0116-33.220823.415764.1792
20.47790.1527-0.3670.4625-0.40863.6080.00070.0309-0.0012-0.07490.0614-0.01210.0411-0.0032-0.0620.08-0.01090.01070.04850.01290.0199-37.230818.890537.0763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 496
2X-RAY DIFFRACTION2B1 - 213

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