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- EMDB-9104: Cryo-EM structure of the Ceru+32/GFP-17 protomer -

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Basic information

Entry
Database: EMDB / ID: 9104
TitleCryo-EM structure of the Ceru+32/GFP-17 protomer
Map dataThe structure of a highly symmetrical, well-defined 16-mer formed by 8 Ceru+32 and 8 GFP-17
SampleCeru+32/GFP-17 protomer:
Ceru+32 / GFP-17
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage / Green fluorescent protein
Function and homology information
SourceAequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / 3.47 Å resolution
AuthorsSimon AJ / Zhou Y / Ramasubramani V / Glaser J / Pothukuchy A / Golihar J / Gerberich JC / Leggere JC / Morrow BR / Jung C / Glotzer SC / Taylor DW / Ellington AD
CitationJournal: Nat Chem / Year: 2019
Title: Supercharging enables organized assembly of synthetic biomolecules.
Authors: Anna J Simon / Yi Zhou / Vyas Ramasubramani / Jens Glaser / Arti Pothukuchy / Jimmy Gollihar / Jillian C Gerberich / Janelle C Leggere / Barrett R Morrow / Cheulhee Jung / Sharon C Glotzer / David W Taylor / Andrew D Ellington
Validation ReportPDB-ID: 6mdr

SummaryFull reportAbout validation report
DateDeposition: Sep 5, 2018 / Header (metadata) release: Sep 26, 2018 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Map surface with fitted models
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9104.map.gz (map file in CCP4 format, 44958 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
224 pix
1.1 Å/pix.
= 246.4 Å
224 pix
1.1 Å/pix.
= 246.4 Å
224 pix
1.1 Å/pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.249786 - 0.33042789
Average (Standard dev.)0.00018886346 (0.017410183)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions224224224
Origin0.00.00.0
Limit223.0223.0223.0
Spacing224224224
CellA=B=C: 246.40001 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z246.400246.400246.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.2500.3300.000

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Supplemental data

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Sample components

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Entire Ceru+32/GFP-17 protomer

EntireName: Ceru+32/GFP-17 protomer / Number of components: 3

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Component #1: protein, Ceru+32/GFP-17 protomer

ProteinName: Ceru+32/GFP-17 protomer / Recombinant expression: No
MassTheoretical: 430 kDa
SourceSpecies: Aequorea victoria (jellyfish)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Ceru+32

ProteinName: Ceru+32
Details: Mutations present in the construct but not listed in the mutation list are derived from the reference construct (PDB entry 2B3P).
Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 28.425195 kDa
SourceSpecies: Aequorea victoria (jellyfish)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, GFP-17

ProteinName: GFP-17
Details: Mutations present in the construct but not listed in the mutation list are derived from the reference construct (PDB entry 2B3P).
Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 27.226242 kDa
SourceSpecies: Aequorea victoria (jellyfish)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 126822
3D reconstructionSoftware: RELION / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 2B3P
Overall bvalue: 196
Output model

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