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- EMDB-73168: Structure of the T6SS effector protein PdpC -

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Basic information

Entry
Database: EMDB / ID: EMD-73168
TitleStructure of the T6SS effector protein PdpC
Map dataEM map
Sample
  • Complex: PdpC
    • Protein or peptide: T6SS effector protein PdpC
KeywordsFrancisella / T6SS / secretion / effector / TOXIN
Function / homologyhost cell cytoplasm / Uncharacterized protein
Function and homology information
Biological speciesFrancisella tularensis subsp. novicida (bacteria) / Francisella tularensis subsp. novicida (strain U112) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu X / Zhou ZH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI151055 United States
CitationJournal: To Be Published
Title: Atomic Structure and Phospholipid Binding Properties of the Francisella Type VI Secretion System Effector Protein PdpC
Authors: Liu X / Clemens D / Lee B / Xia X / Fan H / Feng K / Horwitz M / Zhou ZH
History
DepositionOct 10, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73168.png

Downloads & links

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Map

FileDownload / File: emd_73168.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0281
Minimum - Maximum-0.12839516 - 0.19331941
Average (Standard dev.)0.0000179433 (±0.003707393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73168_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 map

Fileemd_73168_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map

Fileemd_73168_half_map_2.map
Annotationhalf2 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 : PdpC

EntireName: PdpC
Components
  • Complex: PdpC
    • Protein or peptide: T6SS effector protein PdpC

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Supramolecule #1: PdpC

SupramoleculeName: PdpC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria)

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Macromolecule #1: T6SS effector protein PdpC

MacromoleculeName: T6SS effector protein PdpC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis subsp. novicida (strain U112) (bacteria)
Strain: U112
Molecular weightTheoretical: 161.288703 KDa
Recombinant expressionOrganism: Francisella tularensis subsp. novicida (strain U112) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSD YKDHDGDYKD HDIDYKDDDD KENLYFQGND KYELNIYFEK IELPKTADFN MISKHDIKEL RVDANLKKK IHLLQFDEDY LAYMRSLRAI HPSKIAMQKI KSIRNKEDSF IIAIFSLDKI IHKTKFISFG HKTVIFDFKK L WGLVDFVI ...String:
MGSSHHHHHH SSGLVPRGSD YKDHDGDYKD HDIDYKDDDD KENLYFQGND KYELNIYFEK IELPKTADFN MISKHDIKEL RVDANLKKK IHLLQFDEDY LAYMRSLRAI HPSKIAMQKI KSIRNKEDSF IIAIFSLDKI IHKTKFISFG HKTVIFDFKK L WGLVDFVI VHTSNKTWVN HKLTSFMPSI TYCNQNIIHL AYHSDFLYIY HTPEFMDDIN VDRENRRELV AKIPDPYWVR AD TKENKIN INSEEENIEK DLKKITKLKN FEISANDIFF SKAIKAAPRL QHKNKSKLFN SLAIENNEKI KRDIIDYAIS NAW YKNEGL LENLMTFLDA LVVRHLYLIA VYSVYEIEIG IKSVKPEYSK LLKAGLLNKD IQNQLIYDQK KISNIIWLGE TFHG LDIEE AEDLCELIDQ GDINPKINPI NPEKLYRAYK ENYGNEALSF REYKEKYNFL DNDKLREEHA NKLSSILEDP KFRVL SYIN AFLCSTKNYL VPYGYLGSNP LTYYNCMLET GKRRTSKEAY FADIRNKLFM VCYLPGFLSS VIADDDFIDW YSNKKE NQE LLKNSYLNNL YKSKQKYIKD FIDLDIIKLL KQTSSQIKPS YIPVAFRYGA FASTTALIRS NANVSNRMEF ELYDSPE RL HNQYSEKEEM IMPKSVNNPK DHSIDNGISL FSLNLTNEKE DGLRKVMLKV AQLYNLDFKV GISGNLDQAM TQALILGM A TTKKNGDILL DEDQMLYMTY LYCIFMAHSV DHTVDEILMS ANTYLLNSEE VKYPIFNIAD FFARPVFGLS KDKEFKSLV EKYENSLKPN SKILKENYIS RVVTLSEVYE VYEDLNCLYS SLSEGSLYNL LSTHSERHCT LLEQYSRKKK AEIGLVQDGE KIKVVNNYS GYAAINQYQR FVSLGRMYDS GAKYSSSHKK QIEKDFNLYL PDKEQINYLK YNFKDNKFDA VYKNKKSKEK N QSHIVYAK KQNTRYCYGY FNDFFVKNRI TTFYKIKDKS GNYLVNLHNE KYSFATPNSD SKIYRVSPEL LNNRDDFKRV SK DIIKSYK YISFDKQKED IVKNFGKNLY HTNYEIWVGL SHQAISCFSV LDNIDTQEAA NTFIDALYYV RLMQLYYGKT IPF LWISSE IVRYSSSETH YYIPTEENFE NILKIALNNA SKPVIERFLI ILNIYNSTID NNALILIRCR LPIILFEYEE QKLK LKALQ KCADSYKKNN YKNEINFSAW FESIFHVQNL SLSPNYIGNN ILILSLVEEL KPKCSEYKKN MINQQITAKA NELNF YQLL IRLIEISTYH RILTKSIITN TTSLLYDILN KPEFQTINKL INKLFIYKNK DLNTDKYKAF HTKLITIEST YKKINS LYK SDFFKKISS

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: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 322627
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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