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- EMDB-51917: Streptavidin map obtained from graphene oxide modified self-wicki... -

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Basic information

Entry
Database: EMDB / ID: EMD-51917
TitleStreptavidin map obtained from graphene oxide modified self-wicking grids
Map data
Sample
  • Organelle or cellular component: Homotetramer of streptavidin
    • Protein or peptide: Streptavidin
KeywordsBiotin binding / UNKNOWN FUNCTION
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: 4.1 Å
AuthorsWeckener M / Darrow MC / Clare DK / Naismith JH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/T011998/1 United Kingdom
CitationJournal: To Be Published
Title: Modifying chameleon self-wicking grids with graphene oxide
Authors: Weckener M / Owen CD / Darrow MC / Clare DK / Naismith JH
History
DepositionOct 28, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51917.png

Downloads & links

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Map

FileDownload / File: emd_51917.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-4.282175 - 7.1719885
Average (Standard dev.)-0.0029081036 (±0.09408583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51917_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_51917_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51917_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51917_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetramer of streptavidin

EntireName: Homotetramer of streptavidin
Components
  • Organelle or cellular component: Homotetramer of streptavidin
    • Protein or peptide: Streptavidin

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Supramolecule #1: Homotetramer of streptavidin

SupramoleculeName: Homotetramer of streptavidin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces avidinii (bacteria)
Molecular weightTheoretical: 64 KDa

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Macromolecule #1: Streptavidin

MacromoleculeName: Streptavidin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces avidinii (bacteria)
SequenceString:
MRKIVVAAIA VSLTTVSITA SASADPSKDS KAQVSAAEAG ITGTWYNQLG STFIVTAGAD GALTGTYES AVGNAESRYV LTGRYDSAPA TDGSGTALGW TVAWKNNYRN AHSATTWSGQ Y VGGAEARI NTQWLLTSGT TEANAWKSTL VGHDTFTKVK PSAASIDAAK KAGVNNGNPL DA VQQ

UniProtKB: Streptavidin

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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

Concentration1 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
25.0 mMTrisTris
75.0 mMNaClSodium chloride
GridModel: SPT Labtech self-wicking R1.2/0.8 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY ARRAY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 77 % / Chamber temperature: 296.65 K / Instrument: SPOTITON
Details: Please change instrument to SPT Labtech chameleon..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
DetailsComa-free alignment in EPU.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9512 / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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: 6719911
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 68255
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsPDB 8hrm was fitted into the map density as a rigid body using chimera.
RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation

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