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- EMDB-50054: Cryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4p -

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Basic information

Entry
Database: EMDB / ID: EMD-50054
TitleCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4p
Map data
Sample
  • Complex: Filament fragment of A4p bound CCaCalpL
    • Complex: CCaCalpL
      • Protein or peptide: SMODS-associated and fused to various effectors domain-containing protein
    • Complex: A4p
      • RNA: A4p (5'-R(*AP*AP*AP*AP)-3')
KeywordsLON PROTEASE / SAVED DOMAIN / CRISPR / HYDROLASE
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / SMODS-associated and fused to various effectors domain-containing protein
Function and homology information
Biological speciesCandidatus Cloacimonas acidaminovorans (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsTamulaitiene G / Sasnauskas G / Smalakyte D / Tamulaitis G
Funding supportLithuania, 1 items
OrganizationGrant numberCountry
Research Council of LithuaniaS-MIP-22-9Lithuania
CitationJournal: To Be Published
Title: Cryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4p
Authors: Smalakyte D / Ruksenaite A / Sasnauskas G / Tamulaitiene G / Tamulaitis G
History
DepositionApr 9, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50054.png

Downloads & links

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Map

FileDownload / File: emd_50054.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-17.810354 - 40.706240000000001
Average (Standard dev.)-0.000000000003779 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_50054_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50054_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50054_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filament fragment of A4p bound CCaCalpL

EntireName: Filament fragment of A4p bound CCaCalpL
Components
  • Complex: Filament fragment of A4p bound CCaCalpL
    • Complex: CCaCalpL
      • Protein or peptide: SMODS-associated and fused to various effectors domain-containing protein
    • Complex: A4p
      • RNA: A4p (5'-R(*AP*AP*AP*AP)-3')

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Supramolecule #1: Filament fragment of A4p bound CCaCalpL

SupramoleculeName: Filament fragment of A4p bound CCaCalpL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: CCaCalpL

SupramoleculeName: CCaCalpL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Candidatus Cloacimonas acidaminovorans (bacteria)

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Supramolecule #3: A4p

SupramoleculeName: A4p / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: SMODS-associated and fused to various effectors domain-containing...

MacromoleculeName: SMODS-associated and fused to various effectors domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: endopeptidase La
Source (natural)Organism: Candidatus Cloacimonas acidaminovorans (bacteria) / Strain: Evry
Molecular weightTheoretical: 63.294172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGGSHHHHHH GMASWSHPQF EKGGHHHHHH GGSGENLYFQ GGSGPKFNET ADKYLKSGSA EAELIILQYI QQDRVSEDDE EWVYNLLEK ANNPYIKLNA LLWLSAKRKY LTQLSKLWGI SENELKSLSQ QQPKIGLFPA VDSRKNAFLA KVFVYKLKSE E PIALAILG ...String:
MGGSHHHHHH GMASWSHPQF EKGGHHHHHH GGSGENLYFQ GGSGPKFNET ADKYLKSGSA EAELIILQYI QQDRVSEDDE EWVYNLLEK ANNPYIKLNA LLWLSAKRKY LTQLSKLWGI SENELKSLSQ QQPKIGLFPA VDSRKNAFLA KVFVYKLKSE E PIALAILG DKIENFSYLA QLGKQNCLIG FNKNIQGNSW QLAVLATLLV KDEKIISKIA YSGIVLPSGE IITAEEIEYK KR CCQNLVH RIKKIEQLDA WLNTETIPLP VIQYQGEENE LKRWQKAMEQ KVQEKFSWFS YELLEDFYGI TNSDLAIFGN GIL PFEANA WQKLLQEQVK DKFKLLEDKV MPKKVLWFYA GQISTLQLGI GALFGFKRAV SILQMEFSNT TYHEVFILYG KENA RQLKN VSVKKEDYQY IQSELLINEP HKNELGFIIY LGSHNPIGEA KAYCQKQLQI NNFLIIQARE NQGVMETSQN WLPYL QEIN SALNTARQEY HWERIHLFQT APTALCMALG IAVGHFLPVD VYHYQFNAEE PKYRCVFSLD KMLNL

UniProtKB: SMODS-associated and fused to various effectors domain-containing protein

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Macromolecule #2: A4p (5'-R(*AP*AP*AP*AP)-3')

MacromoleculeName: A4p (5'-R(*AP*AP*AP*AP)-3') / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.351846 KDa
SequenceString:
AAA(A3P)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4.1) / Number images used: 175826
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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