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- PDB-6tlz: N-Domain P40/P90 Mycoplasma pneumoniae complexed with 3'SL -

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Basic information

Entry
Database: PDB / ID: 6tlz
TitleN-Domain P40/P90 Mycoplasma pneumoniae complexed with 3'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 / beta-lactose / N-acetyl-alpha-neuraminic acid / Mgp-operon protein 3
Function and homology information
Biological speciesMycoplasma pneumoniae M129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 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)209,9325
Polymers208,6472
Non-polymers1,2853
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)104,9753
Polymers104,3241
Non-polymers6522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.212, 107.312, 162.013
Angle α, β, γ (deg.)90.000, 90.120, 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-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-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_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 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: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.1→81.01 Å / Num. obs: 35571 / % possible obs: 97.4 % / Redundancy: 3.1 % / CC1/2: 0.989 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.083 / Rrim(I) all: 0.149 / Rsym value: 0.052 / Net I/σ(I): 5.3
Reflection shellResolution: 3.1→3.27 Å / Rmerge(I) obs: 1.062 / Mean I/σ(I) obs: 1 / Num. unique obs: 5211 / CC1/2: 0.315 / Rpim(I) all: 0.706 / Rrim(I) all: 1.281

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PHASERphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RJ1

6rj1


Resolution: 3.1→81.01 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.496
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1779 5 %RANDOM
Rwork0.244 ---
obs0.245 35548 97.1 %-
Displacement parametersBiso max: 262.85 Å2 / Biso mean: 147.9 Å2 / Biso min: 76.28 Å2
Baniso -1Baniso -2Baniso -3
1-16.9941 Å20 Å21.0529 Å2
2--13.1841 Å20 Å2
3----30.1781 Å2
Refine analyzeLuzzati coordinate error obs: 0.66 Å
Refinement stepCycle: final / Resolution: 3.1→81.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12452 0 86 0 12538
Biso mean--245.06 --
Num. residues----1613
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4354SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2194HARMONIC5
X-RAY DIFFRACTIONt_it12824HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1699SEMIHARMONIC5
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_contact14178SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12824HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg17456HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion1.85
X-RAY DIFFRACTIONt_other_torsion22.88
LS refinement shellResolution: 3.1→3.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2475 50 7.03 %
Rwork0.231 661 -
all0.2321 711 -
obs--97.67 %
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)
110.67675.69472.53846.9892-0.15485.3152-0.45040.86340.9469-0.69110.64050.78750.1807-0.3428-0.19010.1173-0.3043-0.3032-0.28830.176-0.250325.2368-9.940958.8431
29.1794-5.8204-0.42215.876-0.19294.8123-0.3551-0.8812-0.8340.4880.73160.726-0.0225-0.554-0.3765-0.02480.30350.0862-0.24030.2287-0.175526.1067-51.132822.5162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A23 - 996
2X-RAY DIFFRACTION2{ B|* }B23 - 998

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