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- EMDB-20696: Structure of Francisella PdpA-VgrG Complex, Lidded -

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Basic information

Entry
Database: EMDB / ID: EMD-20696
TitleStructure of Francisella PdpA-VgrG Complex, Lidded
Map dataFrancisella PdpA-VgrG Complex, Lidded
Sample
  • Complex: PdpA-VgrG Complex
    • Protein or peptide: PdpA
    • Protein or peptide: VgrG
KeywordsType VI Secretion System / Complex / TRANSPORT PROTEIN
Function / homologysymbiont cell surface / host cell cytoplasm / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesFrancisella tularensis subsp. novicida U112 (bacteria) / Francisella tularensis subsp. novicida (strain U112) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.35 Å
AuthorsYang X / Clemens DL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorAI125497 United States
CitationJournal: Structure / Year: 2019
Title: Atomic Structure of the Francisella T6SS Central Spike Reveals a Unique α-Helical Lid and a Putative Cargo.
Authors: Xue Yang / Daniel L Clemens / Bai-Yu Lee / Yanxiang Cui / Z Hong Zhou / Marcus A Horwitz /
Abstract: Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms ...Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms involved are unknown. Here we report the atomic structure of the Francisella T6SS central spike complex, obtained by cryo-electron microscopy. Our structural and functional studies demonstrate that, unlike the single-protein spike composition of other T6SS subtypes, Francisella T6SS's central spike is formed by two proteins, PdpA and VgrG, akin to T4-bacteriophage gp27 and gp5, respectively, and that PdpA has unique characteristics, including a putative cargo within its cavity and an N-terminal helical lid. Structure-guided mutagenesis demonstrates that the PdpA N-terminal lid and C-terminal spike are essential to Francisella T6SS function. PdpA is thus both an adaptor, connecting VgrG to the tube, and a likely carrier of secreted cargo. These findings are important to understanding Francisella pathogenicity and designing therapeutics to combat tularemia.
History
DepositionSep 8, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseOct 23, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6u9f
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20696.png

Downloads & links

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Map

FileDownload / File: emd_20696.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFrancisella PdpA-VgrG Complex, Lidded
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 350 pix.
= 374.5 Å		1.07 Å/pix.
x 350 pix.
= 374.5 Å		1.07 Å/pix.
x 350 pix.
= 374.5 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: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.09830168 - 0.16501246
Average (Standard dev.)0.00027076312 (±0.0040868693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 374.50003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z374.500374.500374.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0980.1650.000

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Supplemental data

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Sample components

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Entire : PdpA-VgrG Complex

EntireName: PdpA-VgrG Complex
Components
  • Complex: PdpA-VgrG Complex
    • Protein or peptide: PdpA
    • Protein or peptide: VgrG

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Supramolecule #1: PdpA-VgrG Complex

SupramoleculeName: PdpA-VgrG Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Francisella tularensis subsp. novicida U112 (bacteria)

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Macromolecule #1: PdpA

MacromoleculeName: PdpA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis subsp. novicida (strain U112) (bacteria)
Strain: U112
Molecular weightTheoretical: 95.469961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIAVKDITDL NIQDIISQLT SEVINGDTTP SSAKFACEIN SYIINYNLSN INLINTQLKN TKILYRKGLI SKLDYEKYKR YCIISRFKN NIDEFILYFS TNYKDSQSLK IAIKELQNSC SSSLILELPH DYIRKIDVLL TSIDSAIQRS SDLNKTIIKQ L NKLRSSLS ...String:
MIAVKDITDL NIQDIISQLT SEVINGDTTP SSAKFACEIN SYIINYNLSN INLINTQLKN TKILYRKGLI SKLDYEKYKR YCIISRFKN NIDEFILYFS TNYKDSQSLK IAIKELQNSC SSSLILELPH DYIRKIDVLL TSIDSAIQRS SDLNKTIIKQ L NKLRSSLS RYIGYNNVLQ KQEITINIKP INKNFELEDI SFVSTRNKQY FKHNSLTLKN PHIEKLEVCE NIYGINGWLT FD LAYINNH KDFNFLLSPN QPILLDIQIN DSFNFYKKES KKDHHKRTTR FIAIGFNSNS IDIHENFEYS IYSYTKNVSS GVK KFKIQF HDPLKALWTK HKPSYIALNK SLDDIFKDNF FFDSLFSLDT NKSNNLKIRI PQAFISTVNR NFYDFFIQQL EQNK CYLKY FCDKKSGKVS YHVVDQVDND LQRNIVNSDE DLKDKLSPYD ISCFKKQILI SNKSNFYVKE KNICPDVTLN TQRKE DRKI SDTLVKPFSS ILKDNLQSVE YIQSNNDDKQ EIITTGFEIL LTSRNTLPFL DTEITLSKLD NDQNYLLGAT DIKSLY ISQ RKLLFKRSKY CSKQLYENLH NFHYKSDSES DVYEKIAFTK YPSLTHDNSI TYKIKDYSNL TPEYPKYKSF SNFYING RI TIGENVNNDS KKAYKFFKNH KPEESSIAEF QENGEKGTSA ILNSKADILY AIEIAKEMLS DKSSDKPIIY LPLKVNIN S ANNQFIPLRN DDIILIEIQS FTKGEIIELI SNSAISTKKA QQQLLQRQLL GSKENCEMAY TQTSDSETFS LTQVNEDCE NSFLINDKKG IFLRYKSKGN

UniProtKB: Uncharacterized protein

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Macromolecule #2: VgrG

MacromoleculeName: VgrG / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Francisella tularensis subsp. novicida (strain U112) (bacteria)
Strain: U112
Molecular weightTheoretical: 20.539779 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDYKDDDDKD YKDDDDKDYK DDDDKGSKAD HIFNLEEQGL LIDIKDDSKG CTTKLESSGK ITHNATESIE SSADKQIIEN VKDSKISIT EKEILLATKK SSIMLSEDKI VIKIGNSLII LDDSNISLES ATINIKSSAN INIQASQNID IKSLNNSIKA D VNLNAEGL DVNIKGSVTA SIKGSAATMV G

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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3765
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6u9f:
Structure of Francisella PdpA-VgrG Complex, Lidded

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