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- PDB-6tm0: N-Domain P40/P90 Mycoplasma pneumoniae complexed with 6'SL -

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Basic information

Entry
Database: PDB / ID: 6tm0
TitleN-Domain P40/P90 Mycoplasma pneumoniae complexed with 6'SL
ComponentsMgp-operon protein 3
KeywordsCELL ADHESION / Adhesion / extracellular / Sugars
Function / homologyMgpC adhesin / Mgp-operon protein 3, C-terminal domain / MgpC adhesin / MGP3 C-terminal domain / cell adhesion / plasma membrane / 6'-sialyl-lactose / Mgp-operon protein 3
Function and homology information
Biological speciesMycoplasma pneumoniae M129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVizarraga, D. / Aparicio, D. / Illanes, R. / Fita, I. / Perez-Luque, R. / Martin, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: Nat Commun / Year: 2020
Title: Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae.
Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / ...Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / Juliana Esperalba / Miguel Fernández-Huerta / Margot P Scheffer / Jaume Pinyol / Achilleas S Frangakis / Maria Lluch-Senar / Shigetarou Mori / Keigo Shibayama / Tsuyoshi Kenri / Takayuki Kato / Keiichi Namba / Ignacio Fita / Makoto Miyata / David Aparicio /
Abstract: Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which ...Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mgp-operon protein 3
B: Mgp-operon protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,9144
Polymers208,6472
Non-polymers1,2672
Water0
1
A: Mgp-operon protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9572
Polymers104,3241
Non-polymers6341
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mgp-operon protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9572
Polymers104,3241
Non-polymers6341
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.331, 107.380, 160.451
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mgp-operon protein 3 / Mgp3 / ORF-3 protein


Mass: 104323.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae M129 (bacteria) / Gene: MPN_142, MP012 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q50341
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 6'-sialyl-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-lactose
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG3350 and MetOH

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.8→80.22 Å / Num. obs: 47184 / % possible obs: 97 % / Redundancy: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 7.4
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 6819 / CC1/2: 0.252

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
autoXDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RJ1

6rj1


Resolution: 2.8→80.22 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.887 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.37
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2396 5.08 %RANDOM
Rwork0.208 ---
obs0.211 47182 96.8 %-
Displacement parametersBiso max: 219.35 Å2 / Biso mean: 96.22 Å2 / Biso min: 47.57 Å2
Baniso -1Baniso -2Baniso -3
1-12.9549 Å20 Å21.7108 Å2
2---3.9014 Å20 Å2
3----9.0534 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.8→80.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12494 0 86 0 12580
Biso mean--116.04 --
Num. residues----1622
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4352SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2194HARMONIC5
X-RAY DIFFRACTIONt_it12840HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1702SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14533SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12840HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17470HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion23.22
LS refinement shellResolution: 2.8→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2502 31 3.28 %
Rwork0.2335 913 -
all0.2339 944 -
obs--92.68 %
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)
13.81561.0397-1.02711.0105-0.59922.4911-0.27940.2925-0.203-0.13780.1585-0.11980.08910.1180.121-0.1608-0.22610.1045-0.0668-0.0941-0.321233.16169.970358.4249
23.5866-0.92691.01110.8722-0.58872.4257-0.2616-0.26220.17040.11430.1379-0.106-0.10530.09180.1236-0.16830.2115-0.1032-0.0546-0.0901-0.311233.203353.569621.7894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A23 - 998
2X-RAY DIFFRACTION2{ B|* }B23 - 998

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