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- EMDB-42491: CryoEM Structure of Allosterically Switchable De Novo Protein sr3... -

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Basic information

Entry
Database: EMDB / ID: EMD-42491
TitleCryoEM Structure of Allosterically Switchable De Novo Protein sr312, in Open State with Effector Peptide
Map data
Sample
  • Complex: Complex is comprised of 4 sr312 proteins, each sr312 protein is bound to an effector peptide, putting the protein in an open state. Complex is formed with C4 symmetry.
    • Complex: sr312 protein
      • Protein or peptide: sr312
    • Complex: effector peptide
      • Protein or peptide: Effector peptide cs221B
Keywordsde novo / allosterically switchable de novo protein / sr312 / effector peptide / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWeidle C / Skotheim R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature
Title: De novo design of allosterically switchable protein assemblies
Authors: Pillai A / Idris A / Philomin A / Weidle C / Skotheim R / Leung PJY / Broerman A / Demakis C / Borst AJ / Praetorius F / Baker D
History
DepositionOct 25, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_42491.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2375 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.0020858215 - 2.0181763
Average (Standard dev.)0.0023730511 (±0.037460707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 247.49998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex is comprised of 4 sr312 proteins, each sr312 protein is b...

EntireName: Complex is comprised of 4 sr312 proteins, each sr312 protein is bound to an effector peptide, putting the protein in an open state. Complex is formed with C4 symmetry.
Components
  • Complex: Complex is comprised of 4 sr312 proteins, each sr312 protein is bound to an effector peptide, putting the protein in an open state. Complex is formed with C4 symmetry.
    • Complex: sr312 protein
      • Protein or peptide: sr312
    • Complex: effector peptide
      • Protein or peptide: Effector peptide cs221B

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Supramolecule #1: Complex is comprised of 4 sr312 proteins, each sr312 protein is b...

SupramoleculeName: Complex is comprised of 4 sr312 proteins, each sr312 protein is bound to an effector peptide, putting the protein in an open state. Complex is formed with C4 symmetry.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 206.1 KDa

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Supramolecule #2: sr312 protein

SupramoleculeName: sr312 protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: effector peptide

SupramoleculeName: effector peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: sr312

MacromoleculeName: sr312 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.297691 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGTVTFDITN IDWETAEWIM KHVYLIAKKE GTDVTFSFKE GELQITVKNL HEEAKREIEK WIRAAQLAQD PDAESKAEAR KILNELITE KAEELREKTK DEEVRELARE AARLALESDD IEVQRVVLKA LLAALKSKDE EVIRLLLLAA VLAAAAARSG S PEEKLEIA ...String:
SGTVTFDITN IDWETAEWIM KHVYLIAKKE GTDVTFSFKE GELQITVKNL HEEAKREIEK WIRAAQLAQD PDAESKAEAR KILNELITE KAEELREKTK DEEVRELARE AARLALESDD IEVQRVVLKA LLAALKSKDE EVIRLLLLAA VLAAAAARSG S PEEKLEIA KKALELAMKS KDEEVIRLAL LAAVLAARSD DEEVLKKVKE ALEKMERIMD LEDVAREKSG SAEASQAVKE IA DIAEEAL REGLCEVARV ALKRLFKLAK DYPGSDVASL AKKALEKIAE TALRNGCKET AELAKLLLFL LLIIEVVLKM GVR MLTHRG GNAVIVVIEG LHPSQIVQLM QDVIKAAKKL GVTVTITVSG DIVVIMVVVG ASDEEQEEAR RLVQEIARAL QEAK RKGAN EEQLEQLLRE LLERAEREGG SG

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Macromolecule #2: Effector peptide cs221B

MacromoleculeName: Effector peptide cs221B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.091635 KDa
SequenceString:
EERKKELAKE VIETAKKLIE KLAKEE

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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

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
40.0 mMTris - Hydrochloric Acid

Details: 150 mM NaCl, 40 mM Tris, pH 8.0
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 40 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3795 / Average electron dose: 43.0 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: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
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: 971294
Startup modelType of model: INSILICO MODEL / In silico model: Ab Initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 58251
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 12 / Avg.num./class: 4854 / Software - Name: cryoSPARC

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