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- PDB-6rut: Mycoplasma Genitalium Heterodimer Nap Complex (P140-P110 globular) -

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Basic information

Entry
Database: PDB / ID: 6rut
TitleMycoplasma Genitalium Heterodimer Nap Complex (P140-P110 globular)
Components
  • Adhesin P1
  • Mgp-operon protein 3
KeywordsSUGAR BINDING PROTEIN / Adhesion complex
Function / homology
Function and homology information


adhesion of symbiont to microvasculature / cell adhesion / plasma membrane
Similarity search - Function
Adhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal / MgpC adhesin / Mgp-operon protein 3, C-terminal domain / MgpC adhesin / MGP3 C-terminal domain
Similarity search - Domain/homology
Adhesin P1 / Mgp-operon protein 3
Similarity search - Component
Biological speciesMycoplasma genitalium G37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFita, I. / Aparicio, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
CitationJournal: Nat Commun / Year: 2020
Title: Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
Authors: David Aparicio / Margot P Scheffer / Marina Marcos-Silva / David Vizarraga / Lasse Sprankel / Mercè Ratera / Miriam S Weber / Anja Seybert / Sergi Torres-Puig / Luis Gonzalez-Gonzalez / ...Authors: David Aparicio / Margot P Scheffer / Marina Marcos-Silva / David Vizarraga / Lasse Sprankel / Mercè Ratera / Miriam S Weber / Anja Seybert / Sergi Torres-Puig / Luis Gonzalez-Gonzalez / Julian Reitz / Enrique Querol / Jaume Piñol / Oscar Q Pich / Ignacio Fita / Achilleas S Frangakis /
Abstract: Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane ...Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane adhesion complex called Nap comprising proteins P110 and P140. Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. By cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) we find closed and open Nap conformations, determined at 9.8 and 15 Å, respectively. Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. Structural information, in combination with functional studies, suggests a mechanism for attachment and release of M. genitalium to and from the host cell receptor, in which Nap conformations alternate to sustain motility and guarantee infectivity.
History
DepositionMay 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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: Adhesin P1
C: Mgp-operon protein 3
D: Adhesin P1
E: Mgp-operon protein 3
F: Adhesin P1
G: Mgp-operon protein 3
H: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)941,4348
Polymers941,4348
Non-polymers00
Water11,764653
1
A: Mgp-operon protein 3
B: Adhesin P1

G: Mgp-operon protein 3
H: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)470,7174
Polymers470,7174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area13500 Å2
ΔGint-62 kcal/mol
Surface area136600 Å2
MethodPISA
2
C: Mgp-operon protein 3
D: Adhesin P1

E: Mgp-operon protein 3
F: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)470,7174
Polymers470,7174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area13520 Å2
ΔGint-59 kcal/mol
Surface area136240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.000, 157.280, 192.370
Angle α, β, γ (deg.)90.00, 93.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 87378.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: MG192 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22747
#2: Protein
Adhesin P1 / Attachment protein / Cytadhesin P1 / MgPa


Mass: 147979.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: mgpA, MG191 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P20796
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 23% PEG MME 4% PGA 0.1M Sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97897 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2.65→157.28 Å / Num. obs: 189359 / % possible obs: 73.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.32 Å2 / CC1/2: 0.873 / Net I/σ(I): 6.6
Reflection shellResolution: 2.65→2.7 Å / Num. unique obs: 784 / CC1/2: 0.34

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R3T

6r3t


Resolution: 2.65→121.66 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.851 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.366
RfactorNum. reflection% reflectionSelection details
Rfree0.224 9457 4.99 %RANDOM
Rwork0.187 ---
obs0.189 189358 73.2 %-
Displacement parametersBiso mean: 40.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.0661 Å20 Å21.9933 Å2
2---0.4162 Å20 Å2
3---0.3501 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.65→121.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63530 0 0 653 64183
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0165015HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2588435HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d21916SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes11128HARMONIC5
X-RAY DIFFRACTIONt_it65015HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion23.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion8633SEMIHARMONIC5
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_contact72300SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.78 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2641 178 4.7 %
Rwork0.2153 3610 -
all0.2176 3788 -
obs--11.07 %
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)
10.10560.08520.03130.1274-0.01650.02740.0092-0.0078-0.0393-0.0064-0.01130.03860.00320.00510.0021-0.03280.00240.0139-0.0383-0.02320.041945.880610.298956.9151
20.00550.0576-0.043200.17090.05110.00620.01480.02260.01980.01290.0048-0.00440.0279-0.0191-0.0142-0.01050.0494-0.04680.01370.011274.605344.615461.3314
30.01540.0856-0.02590.22510.06980.0107-0.0050.01480.04240.0142-0.0186-0.02880.0066-0.00240.0236-0.0421-0.00630.0212-0.02840.00970.041417.056755.585956.7649
4-0.01560.03280.11260-0.06330.12820.00950.0027-0.00720.0065-0.0037-0.00850.0154-0.0225-0.00580.0145-0.00950.0261-0.0247-0.0084-0.0361-11.6821.307361.3506
50.05070.06760.02420.1530.00520.0967-0.0119-0.0208-0.0101-0.02520.01080.03570.01020.01090.00110.0134-0.00710.039-0.02520.0056-0.021-32.454687.020929.7102
60.0050.1153-0.04190.21630.09950.1307-0.0370.0214-0.0180.01120.0825-0.1328-0.0218-0.0244-0.0456-0.0499-0.04470.07040.0013-0.0608-0.00960.1051117.60234.0784
70.02890.0218-0.08830.18460.02630.2061-0.0022-0.0137-0.0103-0.02640.01520.019-0.03160.0085-0.013-0.01470.0003-0.0123-0.0299-0.0232-0.0001-55.5843136.16229.672
8-0.00150.160.01140.1313-0.06860.0015-0.05370.02320.03230.02230.07920.1520.0380.0448-0.0255-0.1093-0.02150.0053-0.02060.0120.0992-88.0975105.63534.103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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