[English] 日本語
Yorodumi
- PDB-6rj1: N-Domain P40/P90 Mycoplasma pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rj1
TitleN-Domain P40/P90 Mycoplasma pneumoniae
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 / Mgp-operon protein 3
Function and homology information
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsVizarraga, D. / Aparicio, D. / Illanes, R. / Fita, I.
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
DepositionApr 25, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)208,6472
Polymers208,6472
Non-polymers00
Water1,15364
1
A: Mgp-operon protein 3


Theoretical massNumber of molelcules
Total (without water)104,3241
Polymers104,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mgp-operon protein 3


Theoretical massNumber of molelcules
Total (without water)104,3241
Polymers104,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.796, 114.434, 165.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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 (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / Gene: MPN_142, MP012 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q50341
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG3350 and MetOH

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97927 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: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.65→97.8 Å / Num. obs: 54524 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 83.28 Å2 / Net I/σ(I): 8.6
Reflection shellResolution: 2.65→2.79 Å / Num. unique obs: 7879

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZB

5mzb
PDB Unreleased entry


Resolution: 2.65→82.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 1.017 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.899 / SU Rfree Blow DPI: 0.291 / SU Rfree Cruickshank DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2655 4.88 %RANDOM
Rwork0.214 ---
obs0.215 54428 99.6 %-
Displacement parametersBiso mean: 89.37 Å2
Baniso -1Baniso -2Baniso -3
1--20.9602 Å20 Å20 Å2
2--5.079 Å20 Å2
3---15.8812 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.65→82.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12494 0 0 64 12558
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812825HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0817447HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4342SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2210HARMONIC5
X-RAY DIFFRACTIONt_it12825HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion21.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1679SEMIHARMONIC5
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_contact14422SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.67 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.326 -4.13 %
Rwork0.257 1044 -
all0.2602 1089 -
obs--99.45 %
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)
11.3258-1.06930.38923.0656-0.55851.7084-0.0703-0.0054-0.10620.16350.10960.09240.09540.1055-0.0393-0.1808-0.0072-0.0087-0.1896-0.0038-0.2313-8.714630.526-22.9497
21.3960.8624-0.47644.993-1.14662.6085-0.1189-0.0937-0.1633-0.2472-0.0805-0.06770.3923-0.03110.1994-0.1648-0.02070.0619-0.14290.0181-0.1602-4.433876.650620.9996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more