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- EMDB-7436: Single-Particle reconstruction of DARP14 - A designed protein sca... -

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Basic information

Entry
Database: EMDB / ID: 7436
TitleSingle-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa DARPin proteins - Scaffold
Map dataSingle-Particle reconstruction of DARP14 - A designed protein scaffold displaying ~17kDa DARPin proteins - Scaffold
SampleDARP14:
(DARP14 - Subunit ...) x 4
Function / homology5-carboxymethyl-2-hydroxymuconate isomerase / Tautomerase/MIF superfamily / Cobalamin adenosyltransferase-like / ATP:cob(I)alamin adenosyltransferase, PduO-type / Cobalamin adenosyltransferase-like superfamily / Cobalamin adenosyltransferase / 5-carboxymethyl-2-hydroxymuconate isomerase / 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / aromatic compound catabolic process / Uncharacterized protein / Uncharacterized protein
Function and homology information
Sourcesynthetic construct (others) / Pyrococcus horikoshii OT3 (archaea) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.09 Å resolution
AuthorsGonen S / Liu Y / Yeates TO / Gonen T
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system.
Authors: Yuxi Liu / Shane Gonen / Tamir Gonen / Todd O Yeates
Validation ReportPDB-ID: 6c9i

SummaryFull reportAbout validation report
DateDeposition: Jan 26, 2018 / Header (metadata) release: Feb 21, 2018 / Map release: Mar 21, 2018 / Last update: Apr 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0164
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0164
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6c9i
  • Surface level: 0.0164
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7436.map.gz (map file in CCP4 format, 199345 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
368 pix
0.66 Å/pix.
= 241.04 Å
368 pix
0.66 Å/pix.
= 241.04 Å
368 pix
0.66 Å/pix.
= 241.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.655 Å
Density
Contour Level:0.0164 (by author), 0.0164 (movie #1):
Minimum - Maximum-0.112062104 - 0.15028058
Average (Standard dev.)0.00022611892 (0.0059214467)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions368368368
Origin000
Limit367367367
Spacing368368368
CellA=B=C: 241.04 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6550.6550.655
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z241.040241.040241.040
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.1120.1500.000

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Supplemental data

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Sample components

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Entire DARP14

EntireName: DARP14 / Number of components: 5

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Component #1: protein, DARP14

ProteinName: DARP14 / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #2: protein, DARP14 - Subunit A

ProteinName: DARP14 - Subunit A / Recombinant expression: No
SourceSpecies: Pyrococcus horikoshii OT3 (archaea)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, DARP14 - Subunit B

ProteinName: DARP14 - Subunit B / Recombinant expression: No
SourceSpecies: Pseudomonas aeruginosa PAO1 (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #4: protein, DARP14 - Subunit A with DARPin

ProteinName: DARP14 - Subunit A with DARPin / Recombinant expression: No
MassTheoretical: 18.229264 kDa
Source (engineered)Expression System: Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3

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Component #5: protein, DARP14 - Subunit B

ProteinName: DARP14 - Subunit B / Recombinant expression: No
MassTheoretical: 14.346274 kDa
Source (engineered)Expression System: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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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: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: T (tetrahedral) / Number of projections: 34650
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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