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

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Basic information

Database: EMDB / ID: 3611
TitleFull-length dodecameric S. typhimurium Wzz complex with associated dodecyl maltoside micelle.
SampleDodecameric complex
SourceStaphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
Map dataWzz dodecamer with dodecyl maltoside micelle
Methodsingle particle reconstruction, at 9 Å resolution
AuthorsFord RC / Kargas V
CitationStructure, 2017, 25, 806-815.e3

Structure, 2017, 25, 806-815.e3 StrPapers
Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States.
Richard F Collins / Vasileios Kargas / Brad R Clarke / C Alistair Siebert / Daniel K Clare / Peter J Bond / Chris Whitfield / Robert C Ford

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

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5nbz
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-128-128-128
D min/max/mean-3.2244.5610.027

Supplemental data

Sample components

Entire Dodecameric complex

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

Component #1: protein, Dodecameric complex

ProteinName: Dodecameric complex / Recombinant expression: No
MassTheoretical: 360 kDa
SourceSpecies: Staphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Component #2: protein, WzzB

ProteinName: WzzB / Recombinant expression: No
MassTheoretical: 26.760129 kDa
Source (engineered)Expression System: Staphylococcus aureus / bacteria / スタフィロコッカス・アウレウス, 黄色ブドウ球菌

Experimental details

Sample preparation

Specimen stateparticle
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

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
CameraDetector: GATAN K2 (4k x 4k)

Image processing

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

Atomic model buiding

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

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