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- EMDB-3611: Full-length dodecameric S. typhimurium Wzz complex with associate... -

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Basic information

Entry
Database: EMDB / ID: 3611
TitleFull-length dodecameric S. typhimurium Wzz complex with associated dodecyl maltoside micelle.
Map dataWzz dodecamer with dodecyl maltoside micelle
SampleDodecameric complex
  • WzzB
SourceStaphylococcus aureus / / bacteria
Methodsingle particle reconstruction / cryo EM / 9 Å resolution
AuthorsFord RC / Kargas V
CitationJournal: Structure / Year: 2017
Title: Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States.
Authors: Richard F Collins / Vasileios Kargas / Brad R Clarke / C Alistair Siebert / Daniel K Clare / Peter J Bond / Chris Whitfield / Robert C Ford
Abstract: Wzz is an integral inner membrane protein involved in regulating the length of lipopolysaccharide O-antigen glycans and essential for the virulence of many Gram-negative pathogens. In all Wzz ...Wzz is an integral inner membrane protein involved in regulating the length of lipopolysaccharide O-antigen glycans and essential for the virulence of many Gram-negative pathogens. In all Wzz homologs, the large periplasmic domain is proposed to be anchored by two transmembrane helices, but no information is available for the transmembrane and cytosolic domains. Here we have studied purified oligomeric Wzz complexes using cryoelectron microscopy and resolved the transmembrane regions within a semi-continuous detergent micelle. The transmembrane helices of each monomer display a right-handed super-helical twist, and do not interact with the neighboring transmembrane domains. Modeling, flexible fitting and multiscale simulation approaches were used to study the full-length complex and to provide explanations for the influence of the lipid bilayer on its oligomeric status. Based on structural and in silico observations, we propose a new mechanism for O-antigen chain-length regulation that invokes synergy of Wzz and its polymerase partner, Wzy.
Copyright: 2017 Elsevier Ltd. All rights reserved.
Validation ReportPDB-ID: 5nbz

SummaryFull reportAbout validation report
DateDeposition: Mar 2, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 5, 2017 / Last update: Jun 28, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
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  • Surface view colored by cylindrical radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: : PDB-5nbz
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5nbz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3611.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.45 Å/pix.
= 371.2 Å
256 pix
1.45 Å/pix.
= 371.2 Å
256 pix
1.45 Å/pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:0.66 (by author), 1 (movie #1):
Minimum - Maximum-3.2235954 - 4.561451
Average (Standard dev.)0.026504155 (0.2090128)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 371.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-3.2244.5610.027

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Supplemental data

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Sample components

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Entire Dodecameric complex

EntireName: Dodecameric complex / Number of components: 2
MassTheoretical: 360 kDa

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Component #1: protein, Dodecameric complex

ProteinName: Dodecameric complex / Recombinant expression: No
MassTheoretical: 360 kDa
SourceSpecies: Staphylococcus aureus / / bacteria
Source (engineered)Expression System: Escherichia coli / / bacteria /

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Component #2: protein, WzzB

ProteinName: WzzB / Recombinant expression: No
MassTheoretical: 26.760129 kDa
Source (engineered)Expression System: Staphylococcus aureus / / bacteria

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml
Buffer solution: 20mM Tris pH 7.5, 150mM NaCl, 0.025% dodecyl maltoside.
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 95 % / Details: 1 x 4sec blot

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 22000
3D reconstructionResolution: 9 Å / Resolution method: OTHER / Details: ResMap

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL / Input PDB model: 4E29
Chain ID: 4E29_A
Output model

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