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- EMDB-0689: The reconstruction of biotin-bound streptavidin at 3.2 Angstrom r... -

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Basic information

Entry
Database: EMDB / ID: EMD-0689
TitleThe reconstruction of biotin-bound streptavidin at 3.2 Angstrom resolution
Map data
Sample
  • Complex: Streptavidin with biotin
    • Protein or peptide: Streptavidin
  • Ligand: BIOTIN
  • Ligand: water
Keywordsstreptavidin / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFan X / Wang J / Lei JL / Wang HW
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 to H.W. China
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.
History
DepositionJan 15, 2019-
Header (metadata) releaseMay 29, 2019-
Map releaseMay 29, 2019-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j6j
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0689.png

Downloads & links

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Map

FileDownload / File: emd_0689.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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.35063443 - 0.48228425
Average (Standard dev.)0.00063843746 (±0.020475361)
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-0.3510.4820.001

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Supplemental data

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Sample components

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Entire : Streptavidin with biotin

EntireName: Streptavidin with biotin
Components
  • Complex: Streptavidin with biotin
    • Protein or peptide: Streptavidin
  • Ligand: BIOTIN
  • Ligand: water

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Supramolecule #1: Streptavidin with biotin

SupramoleculeName: Streptavidin with biotin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces avidinii (bacteria)
Molecular weightTheoretical: 52 KDa

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Macromolecule #1: Streptavidin

MacromoleculeName: Streptavidin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces avidinii (bacteria)
Molecular weightTheoretical: 12.596641 KDa
SequenceString:
GITGTWYNQL GSTFIVTAGA DGALTGTYES AVGNAESRYV LTGRYDSAPA TDGSGTALGW TVAWKNNYRN AHSATTWSGQ YVGGAEARI NTQWLLTSGT TEANAWKSTL VGHDTFTKVK

UniProtKB: Streptavidin

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Macromolecule #2: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 2 / Number of copies: 4 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mM(HOCH2)3CNH2Tris-HCl
75.0 mMNaClSodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Spherical aberration corrector: spherical aberration corrector
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 1450 / Average exposure time: 2.56 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: -0.8 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1346980
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Relion 3D initial model reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 45686
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Avg.num./class: 54017 / Software - Name: RELION
FSC plot (resolution estimation)

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