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- PDB-7dyr: CryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (... -

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Basic information

Entry
Database: PDB / ID: 7dyr
TitleCryoEM Structure of Mannose Transporter ManYZ and Microcin E492 (MceA) complex
Components
  • Microcin E492
  • PTS system mannose-specific EIIC component
  • PTS system mannose-specific EIID component
KeywordsPROTEIN TRANSPORT / MceA / Microcin E492 / Bacteriocin / PTS / ManYZ / transporter / Mannose
Function / homology
Function and homology information


mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / cytolysis / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / monoatomic ion transport / defense response to bacterium / membrane / plasma membrane
Similarity search - Function
Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile.
Similarity search - Domain/homology
alpha-D-mannopyranose / PTS system mannose-specific EIIC component / PTS system mannose-specific EIID component / Microcin E492
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Klebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsWang, J.W. / Zeng, J.W.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
National Natural Science Foundation of China (NSFC)31621092 China
CitationJournal: Cell Discov / Year: 2021
Title: Structure of the mannose phosphotransferase system (man-PTS) complexed with microcin E492, a pore-forming bacteriocin.
Authors: Kai Huang / Jianwei Zeng / Xueli Liu / Tianyu Jiang / Jiawei Wang /
History
DepositionJan 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
Y: PTS system mannose-specific EIIC component
Z: PTS system mannose-specific EIID component
A: Microcin E492
B: PTS system mannose-specific EIIC component
C: PTS system mannose-specific EIID component
D: Microcin E492
E: PTS system mannose-specific EIIC component
F: PTS system mannose-specific EIID component
G: Microcin E492
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,09612
Polymers199,5559
Non-polymers5403
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47910 Å2
ΔGint-451 kcal/mol
Surface area64340 Å2

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Components

#1: Protein PTS system mannose-specific EIIC component / EII-P-Man / EIIC-Man / Mannose permease IIC component


Mass: 27647.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: manY, pel, ptsP, b1818, JW1807 / Variant: K-12
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): BL21 / References: UniProt: P69801
#2: Protein PTS system mannose-specific EIID component / EII-M-Man / EIID-Man / Mannose permease IID component


Mass: 30983.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: manZ, gptB, ptsM, b1819, JW1808 / Variant: K-12
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): BL21 / References: UniProt: P69805
#3: Protein Microcin E492 / MccE492


Mass: 7887.492 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: mceA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Z4N4
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ManYZ trimer complex with Microcin E492 (MceA) / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.53 kDa/nm / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92076 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00813875
ELECTRON MICROSCOPYf_angle_d0.76518945
ELECTRON MICROSCOPYf_dihedral_angle_d20.0252130
ELECTRON MICROSCOPYf_chiral_restr0.0512340
ELECTRON MICROSCOPYf_plane_restr0.0062328

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