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- EMDB-9906: Structure of membrane protein -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-9906
TitleStructure of membrane protein
Map data
Sample
  • Complex: ManYZ trimer complex
    • Protein or peptide: PTS mannose transporter subunit IID
    • Protein or peptide: PTS system mannose-specific EIIC component
  • Ligand: alpha-D-mannopyranose
KeywordsPTS / ManYZ / transporter / Mannose / PROTEIN TRANSPORT
Function / homology
Function and homology information


mannose transmembrane transport / N-acetylglucosamine transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / fructose import across plasma membrane / D-glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / 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
: / PTS system mannose-specific EIIC component / PTS system mannose-specific EIID component
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli str. K-12 substr. MG1655 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsWang JW / Zeng JW
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)No. 2016YFA0501103 China
Ministry of Science and Technology (MoST, China)2015CB910104 China
National Natural Science Foundation of China (NSFC)31621092 China
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 /
History
DepositionMay 10, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseJul 10, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k1h
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9906.png

Downloads & links

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Map

FileDownload / File: emd_9906.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 200 pix.
= 267.6 Å		1.34 Å/pix.
x 200 pix.
= 267.6 Å		1.34 Å/pix.
x 200 pix.
= 267.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.37380853 - 0.56950754
Average (Standard dev.)0.0008224773 (±0.014518512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 267.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z267.600267.600267.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.3740.5700.001

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Supplemental data

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Sample components

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Entire : ManYZ trimer complex

EntireName: ManYZ trimer complex
Components
  • Complex: ManYZ trimer complex
    • Protein or peptide: PTS mannose transporter subunit IID
    • Protein or peptide: PTS system mannose-specific EIIC component
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: ManYZ trimer complex

SupramoleculeName: ManYZ trimer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 176 kDa/nm

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Macromolecule #1: PTS mannose transporter subunit IID

MacromoleculeName: PTS mannose transporter subunit IID / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Molecular weightTheoretical: 30.983373 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MVDTTQTTTE KKLTQSDIRG VFLRSNLFQG SWNFERMQAL GFCFSMVPAI RRLYPENNEA RKQAIRRHLE FFNTQPFVAA PILGVTLAL EEQRANGAEI DDGAINGIKV GLMGPLAGVG DPIFWGTVRP VFAALGAGIA MSGSLLGPLL FFILFNLVRL A TRYYGVAY ...String:
MVDTTQTTTE KKLTQSDIRG VFLRSNLFQG SWNFERMQAL GFCFSMVPAI RRLYPENNEA RKQAIRRHLE FFNTQPFVAA PILGVTLAL EEQRANGAEI DDGAINGIKV GLMGPLAGVG DPIFWGTVRP VFAALGAGIA MSGSLLGPLL FFILFNLVRL A TRYYGVAY GYSKGIDIVK DMGGGFLQKL TEGASILGLF VMGALVNKWT HVNIPLVVSR ITDQTGKEHV TTVQTILDQL MP GLVPLLL TFACMWLLRK KVNPLWIIVG FFVIGIAGYA CGLLGL

UniProtKB: UNIPROTKB: A0A387CW08

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Macromolecule #2: PTS system mannose-specific EIIC component

MacromoleculeName: PTS system mannose-specific EIIC component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 28.752783 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MEITTLQIVL VFIVACIAGM GSILDEFQFH RPLIACTLVG IVLGDMKTGI IIGGTLEMIA LGWMNIGAAV APDAALASII STILVIAGH QSIGAGIALA IPLAAAGQVL TIIVRTITVA FQHAADKAAD NGNLTAISWI HVSSLFLQAM RVAIPAVIVA L SVGTSEVQ ...String:
MEITTLQIVL VFIVACIAGM GSILDEFQFH RPLIACTLVG IVLGDMKTGI IIGGTLEMIA LGWMNIGAAV APDAALASII STILVIAGH QSIGAGIALA IPLAAAGQVL TIIVRTITVA FQHAADKAAD NGNLTAISWI HVSSLFLQAM RVAIPAVIVA L SVGTSEVQ NMLNAIPEVV TNGLNIAGGM IVVVGYAMVI NMMRAGYLMP FFYLGFVTAA FTNFNLVALG VIGTVMAVLY IQ LSPKYNR VAGAPAQAAG NNDLDNELDH HHHHHHH

UniProtKB: PTS system mannose-specific EIIC component

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Macromolecule #3: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 309996
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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