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- PDB-6zlv: MreC -

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Basic information

Entry
Database: PDB / ID: 6zlv
TitleMreC
ComponentsRod shape-determining protein MreC
KeywordsSTRUCTURAL PROTEIN / bacterial cell wall elongation
Function / homology
Function and homology information


regulation of cell shape / plasma membrane
Similarity search - Function
Rod shape-determining protein MreC, domain 2 / : / Cell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / Rod shape-determining protein MreC, barrel core / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cell shape-determining protein MreC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsEstrozi, L.F. / Contreras-Martel, C.
Funding support Brazil, France, 7items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/52067-6 Brazil
Sao Paulo Research Foundation (FAPESP)2017/12436-9 Brazil
French National Research AgencyANR-18-CE11-0019 France
Foundation for Medical Research (France)DEQ20170336705 France
Sao Paulo Research Foundation (FAPESP)2015/19906-5 Brazil
French National Research AgencyANR-10-INBS-05-02 France
French National Research AgencyANR-17-EURE-0003 France
CitationJournal: Nat Commun / Year: 2021
Title: Self-association of MreC as a regulatory signal in bacterial cell wall elongation.
Authors: Alexandre Martins / Carlos Contreras-Martel / Manon Janet-Maitre / Mayara M Miyachiro / Leandro F Estrozi / Daniel Maragno Trindade / Caíque C Malospirito / Fernanda Rodrigues-Costa / ...Authors: Alexandre Martins / Carlos Contreras-Martel / Manon Janet-Maitre / Mayara M Miyachiro / Leandro F Estrozi / Daniel Maragno Trindade / Caíque C Malospirito / Fernanda Rodrigues-Costa / Lionel Imbert / Viviana Job / Guy Schoehn / Ina Attrée / Andréa Dessen /
Abstract: The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the ...The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the cytoskeletal element MreB and regulates the activity of cell wall biosynthesis enzymes, in a process that may be dependent on MreC self-association. Here, we use electron cryo-microscopy and X-ray crystallography to determine the structure of a self-associated form of MreC from Pseudomonas aeruginosa in atomic detail. MreC monomers interact in head-to-tail fashion. Longitudinal and lateral interfaces are essential for oligomerization in vitro, and a phylogenetic analysis of proteobacterial MreC sequences indicates the prevalence of the identified interfaces. Our results are consistent with a model where MreC's ability to alternate between self-association and interaction with the cell wall biosynthesis machinery plays a key role in the regulation of elongasome activity.
History
DepositionJul 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / em_admin / em_entity_assembly_recombinant / entity_src_gen / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _em_entity_assembly_recombinant.ncbi_tax_id / _em_entity_assembly_recombinant.organism / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Jul 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / refine / struct_ncs_dom_lim
Item: _em_admin.last_update / _refine.ls_d_res_high ..._em_admin.last_update / _refine.ls_d_res_high / _refine.ls_d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Rod shape-determining protein MreC
B: Rod shape-determining protein MreC
C: Rod shape-determining protein MreC
D: Rod shape-determining protein MreC


Theoretical massNumber of molelcules
Total (without water)76,2194
Polymers76,2194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6660 Å2
ΔGint-13 kcal/mol
Surface area30570 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 79 - 254 / Label seq-ID: 1 - 176

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Rod shape-determining protein MreC


Mass: 19054.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mreC, GNQ20_16665 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6A9K3A1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: MreC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 1200
Image scansMovie frames/image: 20 / Used frames/image: 2-20

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Processing

SoftwareName: REFMAC / Version: 5.8.0258 / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 62.997637589 ° / Axial rise/subunit: 10.35 Å / Axial symmetry: D2
Particle selectionNum. of particles selected: 111624
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91840 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
RefinementResolution: 3.5→3.5 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 47.116 / SU ML: 0.604 / ESU R: 0.783
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.28244 --
obs0.28244 30441 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 127.025 Å2
Baniso -1Baniso -2Baniso -3
1-12.1 Å2-17.71 Å21.3 Å2
2--0.16 Å21.54 Å2
3----12.26 Å2
Refinement stepCycle: 1 / Total: 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0125432
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.7321.6347396
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.2365700
ELECTRON MICROSCOPYr_dihedral_angle_2_deg26.75821.571280
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.92415908
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.7941548
ELECTRON MICROSCOPYr_chiral_restr0.1020.2716
ELECTRON MICROSCOPYr_gen_planes_refined0.010.024124
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it16.57611.262812
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it26.31416.8643508
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it23.70713.6982620
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined49.06621443
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A108160.01
12B108160.01
21A108100
22C108100
31A108140
32D108140
41B108220
42C108220
51B108220.01
52D108220.01
61C108080
62D108080
LS refinement shellResolution: 3.6→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.512 2274 -
obs--100 %

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