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Entry
Database: EMDB / ID: EMD-8005
TitleResolution and Probabilistic Structural Models of Subcomponents Derived from CryoEM Maps of Mature P22 Bacteriophage
Map dataP22 mature virion
Sample
  • Virus: Enterobacteria phage P22 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Peptidoglycan hydrolase gp4
    • Protein or peptide: Tail fiber protein
Keywordsvirion / portal / tailspike / adhesin / VIRAL PROTEIN
Function / homology
Function and homology information


viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / virus tail ...viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion assembly / hydrolase activity / virion attachment to host cell
Similarity search - Function
Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding ...Tail accessory factor GP4 / Peptidoglycan hydrolase Gp4 superfamily / P22 tail accessory factor / Phage P22-like portal protein / Phage P22-like portal protein / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Tail spike protein / Portal protein / Peptidoglycan hydrolase gp4
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsPintilie G / Chen DH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Eye Institute (NIH/NEI)PN2EY016525 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
CitationJournal: Biophys J / Year: 2016
Title: Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.
Authors: Grigore Pintilie / Dong-Hua Chen / Cameron A Haase-Pettingell / Jonathan A King / Wah Chiu /
Abstract: CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it ...CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions, which can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 Å), whereas other components are at slightly lower resolutions: portal (9.2 Å), hub (8.5 Å), tailspike (10.9 Å), and needle (10.5 Å). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density.
History
DepositionJan 15, 2016-
Header (metadata) releaseFeb 17, 2016-
Map releaseFeb 17, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gai
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gai
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5gai
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8005.png

Downloads & links

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Map

FileDownload / File: emd_8005.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationP22 mature virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.55 Å/pix.
x 512 pix.
= 1305.6 Å		2.55 Å/pix.
x 512 pix.
= 1305.6 Å		2.55 Å/pix.
x 512 pix.
= 1305.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.55 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.9238281 - 1.4693555
Average (Standard dev.)0.008668718 (±0.063288845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 1305.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.552.552.55
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z1305.6001305.6001305.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ129141209
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-0.9241.4690.009

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Supplemental data

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Additional map: Hub

Fileemd_8005_additional_1.map
AnnotationHub
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tailspikes

Fileemd_8005_additional_2.map
AnnotationTailspikes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Needle

Fileemd_8005_additional_3.map
AnnotationNeedle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Encapsidated DNA

Fileemd_8005_additional_4.map
AnnotationEncapsidated DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: In-portal DNA

Fileemd_8005_additional_5.map
AnnotationIn-portal DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Plug-like densities inside portal

Fileemd_8005_additional_6.map
AnnotationPlug-like densities inside portal
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Other densities in the tail

Fileemd_8005_additional_7.map
AnnotationOther densities in the tail
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Portal

Fileemd_8005_additional_8.map
AnnotationPortal
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Independent Map A

Fileemd_8005_half_map_1.map
AnnotationIndependent Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Independent Map B.

Fileemd_8005_half_map_2.map
AnnotationIndependent Map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterobacteria phage P22

EntireName: Enterobacteria phage P22 (virus)
Components
  • Virus: Enterobacteria phage P22 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Peptidoglycan hydrolase gp4
    • Protein or peptide: Tail fiber protein

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Sci species strain: 13-am H101/C17 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2
Molecular weightTheoretical: 50.7 MDa
Virus shellShell ID: 1 / Name: gp5 / Diameter: 710.0 Å / T number (triangulation number): 7

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage P22 (virus)
Molecular weightTheoretical: 82.397906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ENRLESILSR FDADWTASDE ARREAKNDLF FSRVSQWDDW LSQYTTLQYR GQFDVVRPVV RKLVSEMRQN PIDVLYRPKD GARPDAADV LMGMYRTDMR HNTAKIAVNI AVREQIEAGV GAWRLVTDYE DQSPTSNNQV IRREPIHSAC SHVIWDSNSK L MDKSDARH ...String:
ENRLESILSR FDADWTASDE ARREAKNDLF FSRVSQWDDW LSQYTTLQYR GQFDVVRPVV RKLVSEMRQN PIDVLYRPKD GARPDAADV LMGMYRTDMR HNTAKIAVNI AVREQIEAGV GAWRLVTDYE DQSPTSNNQV IRREPIHSAC SHVIWDSNSK L MDKSDARH CTVIHSMSQN GWEDFAEKYD LDADDIPSFQ NPNDWVFPWL TQDTIQIAEF YEVVEKKETA FIYQDPVTGE PV SYFKRDI KDVIDDLADS GFIKIAERQI KRRRVYKSII TCTAVLKDKQ LIAGEHIPIV PVFGEWGFVE DKEVYEGVVR LTK DGQRLR NMIMSFNADI VARTPKKKPF FWPEQIAGFE HMYDGNDDYP YYLLNRTDEN SGDLPTQPLA YYENPEVPQA NAYM LEAAT SAVKEVATLG VDTEAVNGGQ VAFDTVNQLN MRADLETYVF QDNLATAMRR DGEIYQSIVN DIYDVPRNVT ITLED GSEK DVQLMAEVVD LATGEKQVLN DIRGRYECYT DVGPSFQSMK QQNRAEILEL LGKTPQGTPE YQLLLLQYFT LLDGKG VEM MRDYANKQLI QMGVKKPETP EEQQWLVEAQ QAKQGQQDPA MVQAQGVLLQ GQAELAKAQN QTLSLQIDAA KVEAQNQ LN AARIAEIFNN MDLSKQSEFR EFLKTVASFQ QDRSEDARAN AELLLKGDEQ THKQRMDIAN ILQSQRQNQP SGSVAETP Q

UniProtKB: Portal protein

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Macromolecule #2: Peptidoglycan hydrolase gp4

MacromoleculeName: Peptidoglycan hydrolase gp4 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage P22 (virus)
Molecular weightTheoretical: 15.957813 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TKGDLVRAAL RKLGVASDAT LTDVEPQSMQ DAVDDLEAMM AEWYQDGKGI ITGYVFSDDE NPPAEGDDHG LRSSAVSAVF HNLACRIAP DYALEATAKI IATAKYGKEL LYKQTAISRA KRAPYPSRMP TGSGNSFPNL NEWHYFP

UniProtKB: Peptidoglycan hydrolase gp4

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Macromolecule #3: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
EC number: Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
Source (natural)Organism: Enterobacteria phage P22 (virus)
Molecular weightTheoretical: 71.361875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ANVVVSNPRP IFTESRSFKA VANGKIYIGQ IDTDPVNPAN QIPVYIENED GSHVQITQPL IINAAGKIVY NGQLVKIVTV QGHSMAIYD ANGSQVDYIA NVLKYDPDQY SIEADKKFKY SVKLSDYPTL QDAASAAVDG LLIDRDYNFY GGETVDFGGK V LTIECKAK ...String:
ANVVVSNPRP IFTESRSFKA VANGKIYIGQ IDTDPVNPAN QIPVYIENED GSHVQITQPL IINAAGKIVY NGQLVKIVTV QGHSMAIYD ANGSQVDYIA NVLKYDPDQY SIEADKKFKY SVKLSDYPTL QDAASAAVDG LLIDRDYNFY GGETVDFGGK V LTIECKAK FIGDGNLIFT KLGKGSRIAG VFMESTTTPW VIKPWTDDNQ WLTDAAAVVA TLKQSKTDGY QPTVSDYVKF PG IETLLPP NAKGQNITST LEIRECIGVE VHRASGLMAG FLFRGCHFCK MVDANNPSGG KDGIITFENL SGDWGKGNYV IGG RTSYGS VSSAQFLRNN GGFERDGGVI GFTSYRAGES GVKTWQGTVG STTSRNYNLQ FRDSVVIYPV WDGFDLGADT DMNP ELDRP GDYPITQYPL HQLPLNHLID NLLVRGALGV GFGMDGKGMY VSNITVEDCA GSGAYLLTHE SVFTNIAIID TNTKD FQAN QIYISGACRV NGLRLIGIRS TDGQGLTIDA PNSTVSGITG MVDPSRINVA NLAEEGLGNI RANSFGYDSA AIKLRI HKL SKTLDSGALY SHINGGAGSG SAYTQLTAIS GSTPDAVSLK VNHKDCRGAE IPFVPDIASD DFIKDSSCFL PYWENNS TS LKALVKKPNG ELVRLTLATL

UniProtKB: Tail spike protein

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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: 7.6 / Component - Name: 25 mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Details: Blot for 2 seconds before plunging..

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 100.0 K / Max: 102.0 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN ULTRASCAN 10000 (10k x 10k) / Digitization - Dimensions - Width: 5000 pixel / Digitization - Dimensions - Height: 5000 pixel / Number real images: 1130 / Average electron dose: 25.0 e/Å2
Details: Every image was 2x hardware binned from Gatan 10kx10k CCD.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 70600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 79731
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: MPSA / Number images used: 79731
Initial angle assignmentType: COMMON LINE / Software - Name: MPSA
Final angle assignmentType: COMMON LINE / Software - Name: MPSA
FSC plot (resolution estimation)

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