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- PDB-6s3u: Adhesin P140 from Mycoplasma Genitalium -

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Basic information

Entry
Database: PDB / ID: 6s3u
TitleAdhesin P140 from Mycoplasma Genitalium
ComponentsAdhesin P1
KeywordsPROTEIN BINDING / Adhesion complex
Function / homologyAdhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal / adhesion of symbiont to microvasculature / plasma membrane / Adhesin P1
Function and homology information
Biological speciesMycoplasma genitalium G37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 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
DepositionJun 26, 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
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: Adhesin P1
B: Adhesin P1
C: Adhesin P1
D: Adhesin P1
E: Adhesin P1
F: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)867,9676
Polymers867,9676
Non-polymers00
Water00
1
A: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)144,6611
Polymers144,6611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)144,6611
Polymers144,6611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)144,6611
Polymers144,6611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)144,6611
Polymers144,6611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)144,6611
Polymers144,6611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)144,6611
Polymers144,6611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)459.190, 116.660, 285.640
Angle α, β, γ (deg.)90.00, 124.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Adhesin P1 / Attachment protein / Cytadhesin P1 / MgPa


Mass: 144661.219 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Gene: mgpA, MG191 / Variant: ATCC 33530 / G-37 / NCTC 10195 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20796

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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: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350 0.1M BisTris Propane pH7.5 0.2M Sodium Sulphate Hydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.24→189.88 Å / Num. obs: 123883 / % possible obs: 63.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 80.85 Å2 / CC1/2: 0.986 / Net I/σ(I): 5.8
Reflection shellResolution: 3.24→3.58 Å / Num. unique obs: 6159 / CC1/2: 0.74

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Processing

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

6rut


Resolution: 3.24→37.36 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.52
RfactorNum. reflection% reflectionSelection details
Rfree0.205 6149 5 %RANDOM
Rwork0.184 ---
obs0.185 123103 61.7 %-
Displacement parametersBiso mean: 91.11 Å2
Baniso -1Baniso -2Baniso -3
1--8.1981 Å20 Å2-8.3421 Å2
2--7.6855 Å20 Å2
3---0.5125 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 3.24→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms59769 0 0 0 59769
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0161280HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2783415HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d20601SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes10474HARMONIC5
X-RAY DIFFRACTIONt_it61280HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion24.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion8016SEMIHARMONIC5
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_contact72593SEMIHARMONIC4
LS refinement shellResolution: 3.24→3.45 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3029 121 4.91 %
Rwork0.2483 2342 -
all0.251 2463 -
obs--7.06 %
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)
10.1172-0.03020.25570.7491-0.02560.4835-0.0271-0.1423-0.0033-0.1444-0.0470.1093-0.1368-0.01830.07410.0907-0.117-0.16540.00190.0375-0.1828116.7454131.13352.1954
20.351-0.25750.27880.71140.25170.8590.0951-0.0437-0.0514-0.1419-0.02930.07470.14220.0183-0.06580.1796-0.0852-0.2896-0.1215-0.004-0.245120.640787.240436.1164
30.9217-0.18090.21380.7858-0.0807-0.11770.06210.1221-0.0547-0.1098-0.10790.17380.06490.1630.0457-0.24890.0187-0.0970.03030.12210.087985.887145.379107.9011
41.0711-0.21130.14910.82780.37150.0501-0.07130.00420.2291-0.0138-0.03150.11390.00630.02160.1028-0.46190.0317-0.1884-0.14330.11270.341270.825689.043115.7009
50.0986-0.00780.03030.11270.05410.3592-0.0819-0.11180.129-0.34960.0554-0.136-0.0736-0.10820.02650.2177-0.28620.2913-0.2219-0.04440.1155188.317553.130760.817
60.3641-0.0271-0.09930.17670.03220.25640.1019-0.0873-0.1321-0.17920.0609-0.34230.0807-0.1739-0.16280.1128-0.15510.3149-0.2418-0.30640.152188.98446.037761.638
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|* }

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