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- EMDB-9397: F-pilus/MS2 Maturation protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9397
TitleF-pilus/MS2 Maturation protein complex
Map dataFocused refinement of Escherichia coli F-pilus and Enterobacteria phage MS2 maturation protein.
Sample
  • Complex: F-pilus/MS2 maturation protein complex
    • Complex: Enterobacteria phage MS2 maturation protein
      • Protein or peptide: Maturation protein
    • Complex: F-pilus
      • Protein or peptide: Type IV conjugative transfer system pilin TraA
  • Ligand: (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate
KeywordsMS2 maturation protein / F-pilus / adsorption complex / PROTEIN BINDING
Function / homology
Function and homology information


viral genome circularization / : / virion attachment to host cell pilus / membrane => GO:0016020 / virion component / RNA binding / extracellular region
Similarity search - Function
TraA / TraA / Assembly protein / Phage maturation protein
Similarity search - Domain/homology
Type IV conjugative transfer system pilin TraA / Maturation protein A
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Enterobacteria phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsMeng R / Jiang M / Zhang J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103832 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)U24GM1167 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for the adsorption of a single-stranded RNA bacteriophage.
Authors: Ran Meng / Mengqiu Jiang / Zhicheng Cui / Jeng-Yih Chang / Kailu Yang / Joanita Jakana / Xinzhe Yu / Zhao Wang / Bo Hu / Junjie Zhang /
Abstract: Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of ...Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface. Moreover, binding of the pilus induces slight orientational variations of the Mat relative to the rest of the phage capsid, priming the Mat-connected genomic RNA (gRNA) for its release from the virions. The exposed tip of the attached Mat points opposite to the direction of the pilus retraction, which may facilitate the translocation of the gRNA from the capsid into the host cytosol. In addition, our structures determine the orientation of the assembled F-pilin subunits relative to the cell envelope, providing insights into the F-like type IV secretion systems.
History
DepositionJan 10, 2019-
Header (metadata) releaseFeb 6, 2019-
Map releaseJul 24, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nm5
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nm5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9397.png

Downloads & links

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Map

FileDownload / File: emd_9397.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement of Escherichia coli F-pilus and Enterobacteria phage MS2 maturation protein.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.46 Å/pix.
x 216 pix.
= 531.36 Å		2.46 Å/pix.
x 216 pix.
= 531.36 Å		2.46 Å/pix.
x 216 pix.
= 531.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.18585995 - 0.31311306
Average (Standard dev.)0.00022885329 (±0.0054002595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 531.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.462.462.46
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z531.360531.360531.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.1860.3130.000

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Supplemental data

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Sample components

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Entire : F-pilus/MS2 maturation protein complex

EntireName: F-pilus/MS2 maturation protein complex
Components
  • Complex: F-pilus/MS2 maturation protein complex
    • Complex: Enterobacteria phage MS2 maturation protein
      • Protein or peptide: Maturation protein
    • Complex: F-pilus
      • Protein or peptide: Type IV conjugative transfer system pilin TraA
  • Ligand: (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate

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Supramolecule #1: F-pilus/MS2 maturation protein complex

SupramoleculeName: F-pilus/MS2 maturation protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: F-pilus/MS2 Maturation protein complex

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Supramolecule #2: Enterobacteria phage MS2 maturation protein

SupramoleculeName: Enterobacteria phage MS2 maturation protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: F-pilus

SupramoleculeName: F-pilus / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Enterobacteria phage MS2 (virus)

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Macromolecule #1: Type IV conjugative transfer system pilin TraA

MacromoleculeName: Type IV conjugative transfer system pilin TraA / type: protein_or_peptide / ID: 1 / Number of copies: 75 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.831216 KDa
SequenceString:
QDLMASGNTT VKATFGKDSS VVKWVVLAEV LVGAVMYMMT KNVKFLAGFA IISVFIAVGM AVVGL

UniProtKB: Type IV conjugative transfer system pilin TraA

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Macromolecule #2: Maturation protein

MacromoleculeName: Maturation protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage MS2 (virus)
Molecular weightTheoretical: 44.030934 KDa
SequenceString: MRAFSTLDRE NETFVPSVRV YADGETEDNS FSLKYRSNWT PGRFNSTGAK TKQWHYPSPY SRGALSVTSI DQGAYKRSGS SWGRPYEEK AGFGFSLDAR SCYSLFPVSQ NLTYIEVPQN VANRASTEVL QKVTQGNFNL GVALAEARST ASQLATQTIA L VKAYTAAR ...String:
MRAFSTLDRE NETFVPSVRV YADGETEDNS FSLKYRSNWT PGRFNSTGAK TKQWHYPSPY SRGALSVTSI DQGAYKRSGS SWGRPYEEK AGFGFSLDAR SCYSLFPVSQ NLTYIEVPQN VANRASTEVL QKVTQGNFNL GVALAEARST ASQLATQTIA L VKAYTAAR RGNWRQALRY LALNEDRKFR SKHVAGRWLE LQFGWLPLMS DIQGAYEMLT KVHLQEFLPM RAVRQVGTNI KL DGRLSYP AANFQTTCNI SRRIVIWFYI NDARLAWLSS LGILNPLGIV WEKVPFSFVV DWLLPVGNML EGLTAPVGCS YMS GTVTDV ITGESIISVD APYGWTVERQ GTAKAQISAM HRGVQSVWPT TGAYVKSPFS MVHTLDALAL IRQRLSR

UniProtKB: Maturation protein A

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Macromolecule #3: (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate

MacromoleculeName: (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate / type: ligand / ID: 3 / Number of copies: 70 / Formula: KSV
Molecular weightTheoretical: 200.127 Da
Chemical component information

ChemComp-KSV:
(2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate

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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
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 168989
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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