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- EMDB-15026: Avidin + Biotin-Tempo -

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Basic information

Entry
Database: EMDB / ID: EMD-15026
TitleAvidin + Biotin-Tempo
Map data
Sample
  • Complex: Avidin
    • Protein or peptide: Avidin
  • Ligand: 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide
KeywordsAvidin / Biotin / TEMPO free radical / PROTEIN BINDING
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / 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 speciesGallus gallus (chicken) / chicken (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsMilani J / Myasnikov A / Beckert B / Nazarov S / Ansermet JP / Saenz F
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Other government Switzerland
CitationJournal: To Be Published
Title: Avidin + Biotin-Tempo
Authors: Milani J / Myasnikov A / Beckert B / Nazarov S / Ansermet JP / Saenz F
History
DepositionMay 25, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15026.png

Downloads & links

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Map

FileDownload / File: emd_15026.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.45 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0823641 - 0.18457036
Average (Standard dev.)0.00015028667 (±0.005281436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 172.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15026_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_15026_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_15026_additional_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15026_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_15026_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 : Avidin

EntireName: Avidin
Components
  • Complex: Avidin
    • Protein or peptide: Avidin
  • Ligand: 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide

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Supramolecule #1: Avidin

SupramoleculeName: Avidin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Avidin

MacromoleculeName: Avidin / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: chicken (chicken)
Molecular weightTheoretical: 16.787193 KDa
SequenceString:
MVHATSPLLL LLLLSLALVA PGLSARKCSL TGKWTNDLGS NMTIGAVNSR GEFTGTYITA VTATSNEIKE SPLHGTQNTI NKRTQPTFG FTVNWKFSES TTVFTGQCFI DRNGKEVLKT MWLLRSSVND IGDDWKATRV GINIFTRLRT QKE

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Macromolecule #3: 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a...

MacromoleculeName: 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide
type: ligand / ID: 3 / Number of copies: 4 / Formula: KFL
Molecular weightTheoretical: 412.59 Da
Chemical component information

ChemComp-KFL:
6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide

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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

Concentration4 mg/mL
BufferpH: 7
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 10 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 86.0 K / Max: 100.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 0.9 µm / Calibrated magnification: 311110 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 270000
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: 1421399
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 623000
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 5 / Avg.num./class: 200000 / Details: 2 classes was selected for final refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7zyl:
Avidin + Biotin-Tempo

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