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- EMDB-0690: The reconstruction of apo-state streptavidin at 3.3 Angstrom reso... -

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Basic information

Entry
Database: EMDB / ID: EMD-0690
TitleThe reconstruction of apo-state streptavidin at 3.3 Angstrom resolution
Map data
SampleStreptavidin
Function / homologyAvidin/streptavidin / Avidin / Avidin-like, conserved site / Avidin-like superfamily / Avidin family / Avidin-like domain signature. / Avidin-like domain profile. / extracellular region / Streptavidin
Function and homology information
Biological speciesStreptomyces avidinii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFan X / Wang J / Lei JL / Wang HW
CitationJournal: Nat Commun / Year: 2019
Title: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution.
Authors: Xiao Fan / Jia Wang / Xing Zhang / Zi Yang / Jin-Can Zhang / Lingyun Zhao / Hai-Lin Peng / Jianlin Lei / Hong-Wei Wang /
Abstract: The fast development of single-particle cryogenic electron microscopy (cryo-EM) has made it more feasible to obtain the 3D structure of well-behaved macromolecules with a molecular weight higher than ...The fast development of single-particle cryogenic electron microscopy (cryo-EM) has made it more feasible to obtain the 3D structure of well-behaved macromolecules with a molecular weight higher than 300 kDa at ~3 Å resolution. However, it remains a challenge to obtain the high-resolution structures of molecules smaller than 200 kDa using single-particle cryo-EM. In this work, we apply the Cs-corrector-VPP-coupled cryo-EM to study the 52 kDa streptavidin (SA) protein supported on a thin layer of graphene and embedded in vitreous ice. We are able to solve both the apo-SA and biotin-bound SA structures at near-atomic resolution using single-particle cryo-EM. We demonstrate that the method has the potential to determine the structures of molecules as small as 39 kDa.
Validation ReportPDB-ID: 6j6k

SummaryFull reportAbout validation report
DateDeposition: Jan 15, 2019 / Header (metadata) release: May 29, 2019 / Map release: May 29, 2019 / Update: Jun 19, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.084
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.084
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6j6k
  • Surface level: 0.084
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0690.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 128 pix.
= 134.784 Å
1.05 Å/pix.
x 128 pix.
= 134.784 Å
1.05 Å/pix.
x 128 pix.
= 134.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
Density
Contour LevelBy AUTHOR: 0.084 / Movie #1: 0.084
Minimum - Maximum-0.20867814 - 0.29345104
Average (Standard dev.)0.00061498536 (±0.01209632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 134.784 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0531.0531.053
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z134.784134.784134.784
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2090.2930.001

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Supplemental data

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Sample components

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Entire Streptavidin

EntireName: Streptavidin / Number of components: 2

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Component #1: protein, Streptavidin

ProteinName: Streptavidin / Recombinant expression: No
MassExperimental: 52 kDa
SourceSpecies: Streptomyces avidinii (bacteria)

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Component #2: protein, Streptavidin

ProteinName: Streptavidin / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 12.596641 kDa
SourceSpecies: Streptomyces avidinii (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 285 K / 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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 215000.0 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: -800.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1450 / Sampling size: 5 µm
Raw dataEMPIAR-10269 (Title: Single particle reconstruction of 52 kDa apo-state streptavidin at 3.3 Angstrom resolution
Data size: 2.4 TB
Data #1: Uncorrected apo-state streptavidin movie stacks, binning 2 from super-resolution stacks. [micrographs - multiframe])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2x2 fold dihedral) / Number of projections: 23991
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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