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- PDB-6k1h: Structure of membrane protein -

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Basic information

Entry
Database: PDB / ID: 6k1h
TitleStructure of membrane protein
Components
  • PTS mannose/fructose/sorbose transporter subunit IIC
  • PTS system mannose-specific EIID component
KeywordsPROTEIN TRANSPORT / 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 / phosphoenolpyruvate-dependent sugar phosphotransferase system / integral component of plasma membrane / membrane / plasma membrane
PTS system mannose/fructose/sorbose family IID component / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS_EIID domain profile.
un:a0a387cr27: / PTS system mannose-specific EIID component
Biological speciesEscherichia coli (E. coli)
Escherichia coli str. K-12 substr. MG1655 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsWang, J.W. / Zeng, J.W.
Funding supportChina , 3件
OrganizationGrant numberCountry
Ministry of Science and Technology (China)No. 2016YFA0501103China
Ministry of Science and Technology (China)2015CB910104China
National Natural Science Foundation of China31621092China
CitationJournal: Cell Res. / Year: 2019
Title: Structure of the mannose transporter of the bacterial phosphotransferase system.
Authors: Xueli Liu / Jianwei Zeng / Kai Huang / Jiawei Wang /
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 10, 2019 / Release: Jul 10, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 10, 2019Structure modelrepositoryInitial release
1.1Jul 17, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
Z: PTS system mannose-specific EIID component
Y: PTS mannose/fructose/sorbose transporter subunit IIC
C: PTS system mannose-specific EIID component
B: PTS mannose/fructose/sorbose transporter subunit IIC
F: PTS system mannose-specific EIID component
E: PTS mannose/fructose/sorbose transporter subunit IIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,7499
Polymers179,2086
Non-polymers5403
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area36680 Å2
ΔGint-318 kcal/mol
Surface area62830 Å2

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Components

#1: Protein/peptide 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
#2: Protein/peptide PTS mannose/fructose/sorbose transporter subunit IIC


Mass: 28752.783 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: D8B36_09740 / Variant: K-12
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): BL21 / References: UniProt: A0A387CR27
#3: Chemical ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose

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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 / Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 176 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 309996 / Symmetry type: POINT

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