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- EMDB-49887: Pseudomonas phage Pa223 Portal (C12 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-49887
TitlePseudomonas phage Pa223 Portal (C12 symmetry)
Map data
Sample
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Portal (Connector) protein
KeywordsConstituent protein / Structural protein / Phage tail component / VIRUS
Function / homology: / Phage SU10 portal protein / Portal (Connector) protein
Function and homology information
Biological speciesPseudomonas virus Pa223
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHou CFD / Cingolani G / Lokareddy KR
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM140733 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)OD024978 United States
CitationJournal: To Be Published
Title: High-resolution cryo-EM analysis of the therapeutic Pseudomonas phage Pa223
Authors: Hou CFD / Lokareddy KR / Cingolani G
History
DepositionMar 24, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49887.png

Downloads & links

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Map

FileDownload / File: emd_49887.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.022100182 - 0.06907636
Average (Standard dev.)0.0043493137 (±0.004161331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 484.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49887_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49887_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49887_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas virus Pa223

EntireName: Pseudomonas virus Pa223
Components
  • Virus: Pseudomonas virus Pa223
    • Protein or peptide: Portal (Connector) protein

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Supramolecule #1: Pseudomonas virus Pa223

SupramoleculeName: Pseudomonas virus Pa223 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2590840 / Sci species name: Pseudomonas virus Pa223 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Portal (Connector) protein

MacromoleculeName: Portal (Connector) protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas virus Pa223
Molecular weightTheoretical: 81.180578 KDa
SequenceString: MAKRRRKIKP MDDEQVLRHL DQLVNDALDF NSSELSKQRS EALKYYFGEP FGNERPGKSA IVSRDVQETV DWIMPSLMKV FTSGGQVVK YEPQTAEDVE QAEQETEYVN YLFMRKNEGF KVMFDWFQDT LMMKTGVVKV YVEEVLNPTF ERFSGLSEEM V ADILADPD ...String:
MAKRRRKIKP MDDEQVLRHL DQLVNDALDF NSSELSKQRS EALKYYFGEP FGNERPGKSA IVSRDVQETV DWIMPSLMKV FTSGGQVVK YEPQTAEDVE QAEQETEYVN YLFMRKNEGF KVMFDWFQDT LMMKTGVVKV YVEEVLNPTF ERFSGLSEEM V ADILADPD TEILAQSVDE DGTYSIKIRK DKKKREIKVT CIKPENFLVD RLATCIDDAR FLCHREKYTV SDLRLLGVPE DV LDELPYD EYEFSDSQPE RLVRDNFDMT GQLQYNSGDD AEANREVWAS ECYTLLDVDG DGISELRRIL YVGDYIISNE PWD CRPFAD LNAYRIAHKF HGMSVYDKIR DIQEIRSVLM RNIMDNIYRT NQGRSVVLDG QVNLEDLLTN EAAGIVRVKA MNSI MPLET PQLSGEVYGM LDRLEADRGK RTGITDRTRG LDQNTLHSNQ AAMSVNQLMT AAEQQIDLIA RMFAETGVKR LFQLL HDHA IKYQNQEEVF QLRGKWVAIN PANWRERSDL TVTVGIGNMN KDQQMLHLMR IWEMAQAVVG GGGLGVLVSE QNLYNI LKE VTENAGYKDP DRFWTNPDSP EAQQAKAIRE QKEAQPKPED IKAQADAQRA QSDALAKQAE AQMKQVEAQI RLAEIEL KK QEAVLQQREM ALKEAELQLE RDRFTWERAR NEAEYHLEAT QARAAYIGDG KVPETKKPSK AVRK

UniProtKB: Portal (Connector) 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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 / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 62000
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 46000 / Random conical tilt - Tilt angle: 15 degrees
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46120
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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