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- EMDB-8504: CryoEM structure of the CTP synthase filament at 4.6 Angstrom res... -

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Basic information

Entry
Database: EMDB / ID: 8504
TitleCryoEM structure of the CTP synthase filament at 4.6 Angstrom resolution
SampleCTP synthase filament
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataCTP synthase filament
Methodhelical reconstruction, at 4.6 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 1, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Apr 26, 2017 / Last update: Dec 1, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5u3c
  • Surface level: 2
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_8504.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.22 A/pix
= 390.4 A
320 pix
1.22 A/pix
= 390.4 A
320 pix
1.22 A/pix
= 390.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.22 A
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-3.8410912 - 7.7650504
Average (Standard dev.)6.474641E-9 (0.40380588)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin-160-160-160
Limit159159159
Spacing320320320
CellA=B=C: 390.40002 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.221.221.22
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z390.400390.400390.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-3.8417.7650.000

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Supplemental data

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Sample components

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Entire CTP synthase filament

EntireName: CTP synthase filament
Details: CTP synthase was incubated in the presence of substrates, and filaments form as the product CTP builds up in the reaction.
Number of components: 4

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Component #1: protein, CTP synthase filament

ProteinName: CTP synthase filament
Details: CTP synthase was incubated in the presence of substrates, and filaments form as the product CTP builds up in the reaction.
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: pET22

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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 /

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

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

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

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

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 81.6 A / Delta phi: 48.5 deg.
Sample solutionSpecimen conc.: 0.85 mg/ml / pH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 34 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 / Resolution: 4.6 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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