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- EMDB-54139: Structure of Avast type 5 activator (Gp316, JADA jumbophage protein) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54139
TitleStructure of Avast type 5 activator (Gp316, JADA jumbophage protein)
Map data
Sample
  • Complex: Gp316/JADA homodimer
    • Protein or peptide: Gp316/JADA
Keywordsjumbophage / gp316 / jada / avast5 / dimer / UNKNOWN FUNCTION
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPseudomonas phage vB_PA32_GUMS (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsPacesa M / Muralidharan A / Brouns SJJ
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101003229European Union
CitationJournal: To Be Published
Title: Molecular basis for anti-jumbo phage immunity by AVAST Type V
Authors: Muralidharan A / Rita Costa A / Fierlier D / van den Berg DF / van den Bossche H / Zoumaro-Djayoon A / Pabst M / Pacesa M / Correia BE / Brouns SJJ
History
DepositionJun 23, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54139.png

Downloads & links

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Map

FileDownload / File: emd_54139.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 300 pix.
= 217.8 Å		0.73 Å/pix.
x 300 pix.
= 217.8 Å		0.73 Å/pix.
x 300 pix.
= 217.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00761
Minimum - Maximum-0.08997128 - 0.16553847
Average (Standard dev.)-0.000014700421 (±0.0037218519)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 217.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54139_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54139_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 : Gp316/JADA homodimer

EntireName: Gp316/JADA homodimer
Components
  • Complex: Gp316/JADA homodimer
    • Protein or peptide: Gp316/JADA

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Supramolecule #1: Gp316/JADA homodimer

SupramoleculeName: Gp316/JADA homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage vB_PA32_GUMS (virus)

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Macromolecule #1: Gp316/JADA

MacromoleculeName: Gp316/JADA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PA32_GUMS (virus)
Molecular weightTheoretical: 80.211344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNYAQYNLPV DFESVDTSTF DPNLPNGNYL FSLPLQLSPH QQHPQLQPYF NGVIGLFRLN AQNAATTTQL HAFAYNLLSS NGFQNNYYQ QWAQKVIDFL EFLFIHRQMV NNPQQAMQQA ASLVWSGFVG KCAQTFPQLQ SLVQHLMPNI QQALGVIGQI E SDIQKMRM ...String:
MNYAQYNLPV DFESVDTSTF DPNLPNGNYL FSLPLQLSPH QQHPQLQPYF NGVIGLFRLN AQNAATTTQL HAFAYNLLSS NGFQNNYYQ QWAQKVIDFL EFLFIHRQMV NNPQQAMQQA ASLVWSGFVG KCAQTFPQLQ SLVQHLMPNI QQALGVIGQI E SDIQKMRM GGNTMMQGGY QQPGVQPGSF PGMGAAMGRP GMSSQLPPIN AGIQQTYGQP ATMANPQLNI PGAYTPTTNH DT GPSIANA AYDVPGSSPF LENKPVMQPK DSWGATVEVS PNSSYDTIPG GGDVMILPEL QQNANTVTND NTDLPIPQDV KEL VFDPNY YVPNGFVINK DRPMDVIYNP GGIEIRPAHL VADKPDWVRT ASSANPYSIL MDPAVYCRFL AKWPDNTVHE VYRK WENHM EMDYLKHELQ DDLRRQAHRG GGARTATSYK LSTIMGDAKP VKEVAEEFSP NDAGLTDNRE HDPVILEGYI ACANN LEAE AGALNAVREA LELSEDDVVP AHEYRAASSH PFDASTEVMY EIEDIRKEPD PHLIAKRLKQ LMLDGKLAQR YYRFLV ERL TSAVNEFLAD SMSQKVTIDD FCEDIGDLIA YLIGKKGKSV ADKFTASIPF IVGRSMCVNI DPEEGNSILD LSVRFQT GW RLEELSCLNI YTEKAVLISK LTEPKITQVI MGMAKRLNSS KDSDDARTHK MYIITADGSY LQVIRGALVD NAVLLKLI K

UniProtKB: Uncharacterized 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) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 15624 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1723569
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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