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- EMDB-53820: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its co... -

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Basic information

Entry
Database: EMDB / ID: EMD-53820
TitlePseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
Map data
Sample
  • Complex: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
    • Protein or peptide: Toxin VasX N-terminal region domain-containing protein
    • Protein or peptide: DUF4123 domain-containing protein
KeywordsPseudomonas putida T6SS effector / Pore-Forming Toxin / MIX family domain / adaptor protein / TOXIN
Function / homologyDomain of unknown function DUF4123 / : / Domain of unknown function (DUF4123) / Toxin VasX, N-terminal region / VasX toxin N-terminal region / membrane / DUF4123 domain-containing protein / Toxin VasX N-terminal region domain-containing protein
Function and homology information
Biological speciesPseudomonas putida KT2440 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsVelazquez C / Zabala-Zearreta M / Altuna-Alvarez J / Albesa-Jove D
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-127816NB-I00 Spain
CitationJournal: Embo J. / Year: 2025
Title: Structural insights into the antibacterial function of the Pseudomonas putida effector Tke5
Authors: Velazquez C / Zabala-Zearreta M / Paredes C / Civantos C / Altuna-Alvarez J / Bernal P / Albesa-Jove D
History
DepositionMay 16, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53820.png

Downloads & links

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Map

FileDownload / File: emd_53820.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 600 pix.
= 387.72 Å		0.65 Å/pix.
x 600 pix.
= 387.72 Å		0.65 Å/pix.
x 600 pix.
= 387.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0397
Minimum - Maximum-0.08526547 - 0.17399554
Average (Standard dev.)-0.0001643626 (±0.0021701816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 387.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53820_msk_1.map
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Additional map: #1

Fileemd_53820_additional_1.map
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Half map: #1

Fileemd_53820_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_53820_half_map_2.map
Projections & Slices
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Sample components

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Entire : Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its co...

EntireName: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
Components
  • Complex: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
    • Protein or peptide: Toxin VasX N-terminal region domain-containing protein
    • Protein or peptide: DUF4123 domain-containing protein

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Supramolecule #1: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its co...

SupramoleculeName: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Molecular weightTheoretical: 145 KDa

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Macromolecule #1: Toxin VasX N-terminal region domain-containing protein

MacromoleculeName: Toxin VasX N-terminal region domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Molecular weightTheoretical: 109.903414 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTNASVSSAT SGPACSARVP ILPVRYAIVP RTADAPACRY ADAGFNLEQG FPTLQHSAYT LRALRPGYVY VFMKGPRGEK LVIHEYVGA GLYKELRYQG LEDYHRRERY LSGQSTGWVW ADTCQDTAEE VWIGYSPHLW TNAITARITG SAALRKRHMR Q LDMAELVS ...String:
MTNASVSSAT SGPACSARVP ILPVRYAIVP RTADAPACRY ADAGFNLEQG FPTLQHSAYT LRALRPGYVY VFMKGPRGEK LVIHEYVGA GLYKELRYQG LEDYHRRERY LSGQSTGWVW ADTCQDTAEE VWIGYSPHLW TNAITARITG SAALRKRHMR Q LDMAELVS GNQAPSTQPH VLPVSALQTW VEDFKPTERR MPLTWSSDPV TETLPIGNLH AIARHYPWTQ PKVPVVVALA DA EGMALDL SLSVSAYQHQ LRDLMPAEQL EHTKPAQPPE QERVPACYRL DAEQLSPQSR DFHHRNLVAM LLNKTLESLY PAD APSPEL AAFRLGTSRR GPALSPAESH FQALTHEDYS PNGARLAQRL DVDKYRRFLA ERDALERRIA ALRNLALQAS NDHD AWLAT AEPQHIDNPY SLAAALACYD RDERTSARGL EISLALLIHP MGQPTPGTED HDRRFKRLEQ WLDQHDSPLY TALAP FNPF KDKADSIGTL FGASDNVIEG LAGRFPAMAD ITDLTAQSVN TVVLKRLRGQ TRWDASHGLR RQVQLAAREA NAEKAL GLL AARYRITEQA ITENPFSQEV QRYLKSGMAQ VEEMKALRIS GSRTVSIELT TTARAKPNFL GLLTSGGGGG LNAGMLW FN ILSLKTAYNS LQKSDAPEYT LGFASSVFGV IGAAAATLVS VRATQKAMML KWISTAPGMA FGNGIINFLT SNLFARAS G YPAIIMGFSS DIFKAIRQWQ NGNLISGLYT AAASATTALG SILVLEGSLA IAGTTVLIPF AGWTAAGIAL IGATLIGGG LFLYSKAHSR LHSPLELWAS RSIFGTREND GEIRDNIKLD FDKKLPPFRH IHEEIKSWQI EFFSPKALLA PYSEQLGLGA LTTHLDINN KWPTPDWATI IHTQVTKQNA TLELTILLPE FVVGQSEWSG SLVSQNLDRQ TTPLQINPDC HITQAGLLLH Y KTDARQIR SATLTINYYA NQGLDDDTPS TTTIHLER

UniProtKB: Toxin VasX N-terminal region domain-containing protein

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Macromolecule #2: DUF4123 domain-containing protein

MacromoleculeName: DUF4123 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Molecular weightTheoretical: 35.710516 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SMTTLSSPPP RSEDFAHNCR FLLLMTSAIE NWAYRPIPQE GELVPAYAPS VLDLINAVSR NTQKAWLWKN SALDDRHEF GPLLVDVADA HELLAHAITT WMPIGGAIAL DAEVGLAALA DHFTSLVQVV LPDHSVATHH VTPDHLAAWL N ALDDDHRK ...String:
MGSSHHHHHH SMTTLSSPPP RSEDFAHNCR FLLLMTSAIE NWAYRPIPQE GELVPAYAPS VLDLINAVSR NTQKAWLWKN SALDDRHEF GPLLVDVADA HELLAHAITT WMPIGGAIAL DAEVGLAALA DHFTSLVQVV LPDHSVATHH VTPDHLAAWL N ALDDDHRK AWLGPVSRLA WRVNWGPAHE WKTHENKPIA ARSKSELPLT LQQLELDRLQ AGMHEHFVLS LAHEVLAMPP HA NHTLADI RLWIETLLPQ LTALNFRSEE VAGQFIRLIA GHMWLMSNDK AGKIYTNLEE SPQARLRELQ ALVESKEPAH D

UniProtKB: DUF4123 domain-containing 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

Concentration2.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMTris-HClTris (hydroxymethyl) aminomethane (THAM) hydrochloride
2.0 mMDTTDithiothreitol
0.05 %w/vCHAPS3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Pressure: 0.041 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 381732
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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