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- EMDB-5010: Crystal and cryoEM structural studies of a cell wall degrading en... -

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Basic information

Entry
Database: EMDB / ID: EMD-5010
TitleCrystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail
Map dataThis is an image of a surface rendered top-view of bacteriophage phi29 mutant sus13(342)
Sample
  • Sample: Bacteriophage phi29 mutant sus13(342)
  • Virus: phi29 mutant sus13(342) (unknown)
KeywordsCell wall / phi29 / hydrolase / infection / structure
Biological speciesphi29 mutant sus13(342) (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 35.0 Å
AuthorsXiang Y / Morais MC / Cohen DN / Bowman VD / Anderson DL / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2008
Title: Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail.
Authors: Ye Xiang / Marc C Morais / Daniel N Cohen / Valorie D Bowman / Dwight L Anderson / Michael G Rossmann /
Abstract: The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome ...The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage phi29 is noncontractile and approximately 380 A long. A 1.8-A resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N- and C-terminal domains, whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal end of the phi29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13(-) mutants with the phi29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer.
History
DepositionApr 11, 2008-
Header (metadata) releaseApr 15, 2008-
Map releaseApr 22, 2009-
UpdateNov 23, 2010-
Current statusNov 23, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5010_1.png

Downloads & links

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Map

FileDownload / File: emd_5010.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered top-view of bacteriophage phi29 mutant sus13(342)
Voxel sizeX=Y=Z: 4.24 Å
Density
Contour Level1: 4.5 / Movie #1: 4
Minimum - Maximum-11.447699999999999 - 16.379100000000001
Average (Standard dev.)-0.00804697 (±1.02966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 1272 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.244.244.24
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z1272.0001272.0001272.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-11.44816.379-0.008

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Supplemental data

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Sample components

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Entire : Bacteriophage phi29 mutant sus13(342)

EntireName: Bacteriophage phi29 mutant sus13(342)
Components
  • Sample: Bacteriophage phi29 mutant sus13(342)
  • Virus: phi29 mutant sus13(342) (unknown)

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Supramolecule #1000: Bacteriophage phi29 mutant sus13(342)

SupramoleculeName: Bacteriophage phi29 mutant sus13(342) / type: sample / ID: 1000 / Details: Gene product 13 defect mutant
Oligomeric state: capsid protein forms t3 q5 prolate icosahedron
Number unique components: 8
Molecular weightTheoretical: 35.2 MDa

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Supramolecule #1: phi29 mutant sus13(342)

SupramoleculeName: phi29 mutant sus13(342) / type: virus / ID: 1 / Name.synonym: phi29 mutant sus13(342) / Details: Phi29 gene product 13 defect mutant / Sci species name: phi29 mutant sus13(342) / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: phi29 mutant sus13(342)
Host (natural)Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightTheoretical: 35.2 MDa
Virus shellShell ID: 1 / Name: Phi29 sus13342 / Diameter: 530 Å / T number (triangulation number): 3

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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

Concentration1 mg/mL
BufferpH: 7.8 / Details: 25mM Tris-HCl pH7.8, 50mM NaCl and 5mM MgCl2
GridDetails: holey carbon
VitrificationCryogen name: ETHANE / Chamber temperature: 113 K / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 33000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.3 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 33000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 35 / Average electron dose: 20 e/Å2 / Details: after scanning, images binned by a factor of 2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: phase flip
Final two d classificationNumber classes: 180
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Details: asymmetrical / Number images used: 1390

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Atomic model buiding 1

Initial model(PDB ID:

3csq

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3csr

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3csz

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3ct0

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3ct1

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3ct5

)
RefinementSpace: REAL

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