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- EMDB-54599: Portal and adaptor protein of bacteriophage LUZ19 computed in C12... -

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Basic information

Entry
Database: EMDB / ID: EMD-54599
TitlePortal and adaptor protein of bacteriophage LUZ19 computed in C12 symmetry
Map dataphage LUZ19 portal-adaptor C12 symmetry map
Sample
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: portal protein
    • Protein or peptide: adaptor protein
Keywordsportal protein / adaptor protein / connector / STRUCTURAL PROTEIN
Biological speciesPseudomonas phage LUZ19 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsStefanik Sobotkova A / Cienikova Z / Mironova Y / Fuzik T / Plevka P / Novacek J / Hlavenkova Z
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Structure of bacteriophage LUZ19 native particle
Authors: Stefanik Sobotkova A / Cienikova Z / Mironova Y / Fuzik T / Plevka P / Novacek J / Hlavenkova Z
History
DepositionJul 29, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54599.png

Downloads & links

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Map

FileDownload / File: emd_54599.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphage LUZ19 portal-adaptor C12 symmetry map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0177
Minimum - Maximum-0.09737858 - 0.15965134
Average (Standard dev.)0.00036111753 (±0.005742323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 445.12003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54599_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: phage LUZ19 portal-adaptor C12 symmetry half1 map

Fileemd_54599_half_map_1.map
Annotationphage LUZ19 portal-adaptor C12 symmetry half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: phage LUZ19 portal-adaptor C12 symmetry half2 map

Fileemd_54599_half_map_2.map
Annotationphage LUZ19 portal-adaptor C12 symmetry half2 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 phage LUZ19

EntireName: Pseudomonas phage LUZ19 (virus)
Components
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: portal protein
    • Protein or peptide: adaptor protein

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Supramolecule #1: Pseudomonas phage LUZ19

SupramoleculeName: Pseudomonas phage LUZ19 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 484896 / Sci species name: Pseudomonas phage LUZ19 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 924 KDa

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Macromolecule #1: portal protein

MacromoleculeName: portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 56.169305 KDa
SequenceString: MKTTAAMLWE KLRDGSVESR AIEFAKTTLP YLMVDPMSGS RGVVEHDFQS AGALLVNNLA AKLARSLFPT GIPFFRSELT DAIRREADS RDTDITEVTA ALARVDRKAT QRLFQNASLA VLTQVIKLLI VTGNALLYRD SAAATVVAWS LRSYAVRRDA T GRWMDIVL ...String:
MKTTAAMLWE KLRDGSVESR AIEFAKTTLP YLMVDPMSGS RGVVEHDFQS AGALLVNNLA AKLARSLFPT GIPFFRSELT DAIRREADS RDTDITEVTA ALARVDRKAT QRLFQNASLA VLTQVIKLLI VTGNALLYRD SAAATVVAWS LRSYAVRRDA T GRWMDIVL KQRYKSKDLD EEYKQDLMRA GRNLSGSGSV DLYTHVQRKK GTAMEYAELY HEIDGVRVGK EGRWPIHLCP YI VPTWNLA PGEHYGRGHV EDYIGDFAKL SLLSEKLGLY ELESLEVLNL VDEAKGAVVD DYQDAEMGDY VPGGAEAVRA YER GDYNKM AAIQQSLQAV VVRLNQAFMY GANQRDAERV TAEEVRITAE EAENTLGGTY SLLAENLQSP LAYVCLSEVD DALL QGLIT KQHKPAIETG LPALSRSAAV QSMLNASQVI AGLAPIAQLD PRISLPKMMD TIWAAFSVDT SQFYKSADEL EAEAE QQRQ QAAQAQAAQE TLLEGASDMT NALAGV

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Macromolecule #2: adaptor protein

MacromoleculeName: adaptor protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 21.211096 KDa
SequenceString:
MLLLDAVNVI LRKIGELPIP SMDETYPTMA IALPELEDQR IQLLTQGWWF NTWWRHKLTP DPTGRINLPK GTLAFYPDSP DLQWDGLGV RDANTGDDRI GKPVEGRLVL SREWDHIPEI AQRVIAHQAA LAVYTHEIGP DETAQVIAQE LQAYQNELSR M HTRSRPLN TQAKRSFSRW RRSLRT

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 94.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 21683
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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