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- EMDB-8474: Cryo-EM structure of the human CTP synthase filament -

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Basic information

Entry
Database: EMDB / ID: 8474
TitleCryo-EM structure of the human CTP synthase filament
Samplehuman CTP synthase 1 filament
SourceHomo sapiens / human
Map dataHuman CTP synthase filament
Methodhelical reconstruction, at 6.1 A resolution
AuthorsLynch EM / Kollman JM
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: Nov 22, 2016 / Header (metadata) release: Apr 26, 2017 / Map release: Apr 26, 2017 / Last update: Nov 22, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.8
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5u03
  • Surface level: 3.8
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8474.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.26 A/pix
= 483.84 A
384 pix
1.26 A/pix
= 483.84 A
384 pix
1.26 A/pix
= 483.84 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:3.8 (by author), 3.8 (movie #1):
Minimum - Maximum-8.421113 - 15.893713
Average (Standard dev.)1.69333E-10 (0.6589945)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin-192-192-192
Limit191191191
Spacing384384384
CellA=B=C: 483.84 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.261.261.26
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z483.840483.840483.840
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-8.42115.8940.000

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Supplemental data

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Sample components

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Entire human CTP synthase 1 filament

EntireName: human CTP synthase 1 filament
Details: hCTPS1 filaments assembled in the presence of UTP, ATP, and GTP
Number of components: 4

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Component #1: protein, human CTP synthase 1 filament

ProteinName: human CTP synthase 1 filament
Details: hCTPS1 filaments assembled in the presence of UTP, ATP, and GTP
Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Vector: pDO105-hCTPS1

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Component #2: protein, CTP synthase 1

ProteinName: CTP synthase 1 / Recombinant expression: No
MassTheoretical: 66.777297 kDa
Source (engineered)Expression System: Homo sapiens / human

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

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #4: ligand, URIDINE 5'-TRIPHOSPHATE

LigandName: URIDINE 5'-TRIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.484141 kDa

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 104.1 A / Delta phi: 60.6 deg.
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.9
VitrificationCryogen name: ETHANE

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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)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPIDER, hsearch_lorentz, ctffind / Resolution: 6.1 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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