[English] 日本語
Yorodumi
- EMDB-3611: Full-length dodecameric S. typhimurium Wzz complex with associate... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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

DateDeposition: Mar 2, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 5, 2017 / Last update: Mar 2, 2017

-
Structure visualization

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


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
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 package.

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
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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

-
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
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
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

+
About Yorodumi

-
News

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more