[English] 日本語
Yorodumi
- EMDB-8513: E. coli CTP synthase CC mutant filament (product-bound) -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8513
TitleE. coli CTP synthase CC mutant filament (product-bound)
SampleE. coli CTP synthase CC mutant filament
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataE. coli CTP synthase CC mutant filament (product-bound)
Methodhelical reconstruction, at 5.7 A resolution
AuthorsKollman JM / Lynch EM
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 StrPapers
Human CTP synthase filament structure reveals the active enzyme conformation.
Eric M Lynch / Derrick R Hicks / Matthew Shepherd / James A Endrizzi / Allison Maker / Jesse M Hansen / Rachael M Barry / Zemer Gitai / Enoch P Baldwin / Justin M Kollman

DateDeposition: Dec 8, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Apr 26, 2017 / Last update: Dec 8, 2016

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5u6r
  • Surface level: 2.1
  • 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_8513.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.26 A/pix
= 252. A
200 pix
1.26 A/pix
= 252. A
200 pix
1.26 A/pix
= 252. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.26 A
Density
Contour Level:2.1 (by author), 2.1 (movie #1):
Minimum - Maximum-3.784991 - 7.626205
Average (Standard dev.)1.83376E-10 (0.60962296)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 252 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.261.261.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-3.7857.6260.000

-
Supplemental data

-
Sample components

-
Entire E. coli CTP synthase CC mutant filament

EntireName: E. coli CTP synthase CC mutant filament
Details: Disulfide-crosslinked E. coli CTP synthase filaments assembled in non-reducing buffer, bound to CTP and ADP
Number of components: 4

-
Component #1: protein, E. coli CTP synthase CC mutant filament

ProteinName: E. coli CTP synthase CC mutant filament
Details: Disulfide-crosslinked E. coli CTP synthase filaments assembled in non-reducing buffer, bound to CTP and ADP
Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET22b

-
Component #2: protein, CTP synthase

ProteinName: CTP synthase / Recombinant expression: No
MassTheoretical: 60.44698 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Component #3: ligand, CYTIDINE-5'-TRIPHOSPHATE

LigandName: CYTIDINE-5'-TRIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.483156 kDa

-
Component #4: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

+
Experimental details

-
Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 82.1 A / Delta phi: 48.2 deg.
Sample solutionSpecimen conc.: 0.15 mg/ml / pH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 45 e/A2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPIDER, hsearch_lorentz / Resolution: 5.7 A / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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