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- EMDB-11820: Nonameric cytoplasmic domain of SctV from Yersinia enterocolitica -

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Basic information

Entry
Database: EMDB / ID: EMD-11820
TitleNonameric cytoplasmic domain of SctV from Yersinia enterocolitica
Map dataStructure of the SctV cytoplasmic domain
Sample
  • Complex: Double nonamer of the SctV cytoplasmic domain from Yersinia enterocolitica
    • Protein or peptide: Low calcium response protein
Function / homology
Function and homology information


protein secretion / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family
Similarity search - Domain/homology
Low calcium response protein
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKuhlen L / Johnson S
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust109136 United Kingdom
Wolfson FoundationWL160052 United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: PLoS One / Year: 2021
Title: Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein.
Authors: Lucas Kuhlen / Steven Johnson / Jerry Cao / Justin C Deme / Susan M Lea /
Abstract: Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which ...Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which secretion substrates pass the inner membrane. While the complex formed by four of the EA proteins has been well characterised structurally, little is known about the structure of the membrane domain of the largest subunit, FlhA in flagella, SctV in injectisomes. Furthermore, the biologically relevant nonameric assembly of FlhA/SctV has been infrequently observed and differences in conformation of the cytoplasmic portion of FlhA/SctV between open and closed states have been suggested to reflect secretion system specific differences. FlhA has been shown to bind to chaperone-substrate complexes in an open state, but in previous assembled ring structures, SctV is in a closed state. Here, we identify FlhA and SctV homologues that can be recombinantly produced in the oligomeric state and study them using cryo-electron microscopy. The structures of the cytoplasmic domains from both FlhA and SctV are in the open state and we observe a conserved interaction between a short stretch of residues at the N-terminus of the cytoplasmic domain, known as FlhAL/SctVL, with a groove on the adjacent protomer's cytoplasmic domain, which stabilises the nonameric ring assembly.
History
DepositionOct 7, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0122
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0122
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7alw
  • Surface level: 0.0122
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7alw
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11820.png

Downloads & links

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Map

FileDownload / File: emd_11820.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the SctV cytoplasmic domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 420.864 Å		0.82 Å/pix.
x 512 pix.
= 420.864 Å		0.82 Å/pix.
x 512 pix.
= 420.864 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0112 / Movie #1: 0.0122
Minimum - Maximum-0.024716701 - 0.047070038
Average (Standard dev.)-1.0108143e-07 (±0.001689402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 420.864 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z420.864420.864420.864
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0250.047-0.000

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Supplemental data

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Mask #1

Fileemd_11820_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_11820_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_11820_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Double nonamer of the SctV cytoplasmic domain from Yersinia enter...

EntireName: Double nonamer of the SctV cytoplasmic domain from Yersinia enterocolitica
Components
  • Complex: Double nonamer of the SctV cytoplasmic domain from Yersinia enterocolitica
    • Protein or peptide: Low calcium response protein

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Supramolecule #1: Double nonamer of the SctV cytoplasmic domain from Yersinia enter...

SupramoleculeName: Double nonamer of the SctV cytoplasmic domain from Yersinia enterocolitica
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Yersinia enterocolitica (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 1.4 MDa

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Macromolecule #1: Low calcium response protein

MacromoleculeName: Low calcium response protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Yersinia enterocolitica (bacteria)
Molecular weightTheoretical: 78.667281 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNPHDLEWLN RIGERKDIML AVLLLAVVFM MVLPLPPIVL DILIAVNMTI SVVLLMIAIY INSPLQFSAF PAVLLVTTLF RLALSVSTT RMILLQADAG QIVYTFGNFV VGGNLIVGIV IFLIITIVQF LVITKGSERV AEVSARFSLD AMPGKQMSID G DMRAGVID ...String:
MNPHDLEWLN RIGERKDIML AVLLLAVVFM MVLPLPPIVL DILIAVNMTI SVVLLMIAIY INSPLQFSAF PAVLLVTTLF RLALSVSTT RMILLQADAG QIVYTFGNFV VGGNLIVGIV IFLIITIVQF LVITKGSERV AEVSARFSLD AMPGKQMSID G DMRAGVID VNEARERRAT IEKESQMFGS MDGAMKFVKG DAIAGLIIIF VNILGGVTIG VTQKGLAAAE ALQLYSILTV GD GMVSQVP ALLIAITAGI IVTRVSSEDS SDLGSDIGKQ VVAQPKAMLI GGVLLLLFGL IPGFPTVTFL ILALLVGCGG YML SRKQSR NDEANQDLQS ILTSGSGAPA ARTKAKTSGA NKGRLGEQEA FAMTVPLLID VDSSQQEALE AIALNDELVR VRRA LYLDL GVPFPGIHLR FNEGMGEGEY LISLQEVPVA RGELKAGYLL VRESVSQLEL LGIPYEKGEH LLPDQETFWV SVEYE ERLE KSQLEFFSHS QVLTWHLSHV LREYAEDFIG IQETRYLLEQ MEGGYGELIK EVQRIVPLQR MTEILQRLVG EDISIR NMR SILEAMVEWG QKEKDVVQLT EYIRSSLKRY ICYKYANGNN ILPAYLFDQE VEEKIRSGVR QTSAGSYLAL DPAVTES LL EQVRKTIGDL SQIQSKPVLI VSMDIRRYVR KLIESEYYGL PVLSYQELTQ QINIQPLGRV CLENLYFQ

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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
GridModel: Quantifoil / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D9 (2x9 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 15913
FSC plot (resolution estimation)

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