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- PDB-8h64: Crystal structure of Internalin A from Listeria monocytogenes wit... -

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Basic information

Entry
Database: PDB / ID: 8h64
TitleCrystal structure of Internalin A from Listeria monocytogenes with nanobody VHH24 bound
Components
  • Anti-internalin A VHH24
  • Internalin A
KeywordsCELL INVASION/IMMUNE SYSTEM / Internalin A Cadherin Bacterial invasion nanobody Surface plasmon resonance Isothermal titration calorimetry / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


InlA-mediated entry of Listeria monocytogenes into host cells / peptidoglycan-based cell wall / extracellular region
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 / : / Copper resistance protein CopC/internalin, immunoglobulin-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 / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 15, 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Internalin A
B: Anti-internalin A VHH24
C: Internalin A
D: Anti-internalin A VHH24
E: Internalin A
F: Anti-internalin A VHH24
G: Internalin A
H: Anti-internalin A VHH24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,72512
Polymers253,5838
Non-polymers1424
Water13,079726
1
A: Internalin A
B: Anti-internalin A VHH24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4674
Polymers63,3962
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Internalin A
D: Anti-internalin A VHH24


Theoretical massNumber of molelcules
Total (without water)63,3962
Polymers63,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Internalin A
F: Anti-internalin A VHH24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4313
Polymers63,3962
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Internalin A
H: Anti-internalin A VHH24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4313
Polymers63,3962
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.730, 141.120, 198.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Internalin A


Mass: 49914.758 Da / Num. of mol.: 4
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 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DJM0
#2: Protein
Anti-internalin A VHH24


Mass: 13481.033 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Amonium citrate tribasic pH 7.0; 14% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→62.06 Å / Num. obs: 139561 / % possible obs: 92.1 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.059 / Net I/σ(I): 8.7
Reflection shellResolution: 2.35→2.48 Å / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2 / Num. unique obs: 16169 / CC1/2: 0.721 / Rpim(I) all: 0.365

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8H62 8H63

8h62

8h63


Resolution: 2.35→62.06 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.719 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 7011 5 %RANDOM
Rwork0.1881 ---
obs0.19 132487 91.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.89 Å2 / Biso mean: 38.071 Å2 / Biso min: 11.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å20 Å2
2---0.35 Å20 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.35→62.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17658 0 4 726 18388
Biso mean--59.18 30.79 -
Num. residues----2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01117930
X-RAY DIFFRACTIONr_bond_other_d0.0020.01616497
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.63524494
X-RAY DIFFRACTIONr_angle_other_deg0.5411.54838576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3552317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.603564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.627103081
X-RAY DIFFRACTIONr_chiral_restr0.0710.23059
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023056
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 389 -
Rwork0.285 7740 -
all-8129 -
obs--73.29 %

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