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- EMDB-60944: Cryo-EM structure of Lactobacillus casei DdmE bound with guide an... -

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Basic information

Entry
Database: EMDB / ID: EMD-60944
TitleCryo-EM structure of Lactobacillus casei DdmE bound with guide and target
Map data
Sample
  • Complex: Lactobacillus casei DdmE bound with guide and target
    • DNA: DNA (25-MER)
    • DNA: DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')
    • DNA: DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3')
    • Protein or peptide: DdmE
  • Ligand: MAGNESIUM ION
KeywordsAgo / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Biological speciesLacticaseibacillus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsHuang PP / Chen MR / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: The mechanism of bacterial defense system DdmDE from Lactobacillus casei.
Authors: Pingping Huang / Purui Yan / Lijie Guo / Wenying Fei / Zhaoxing Li / Jingxian Liu / Jianping Kong / Yue Yao / Meiling Lu / Yibei Xiao / Meirong Chen /
History
DepositionJul 25, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60944.png

Downloads & links

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Map

FileDownload / File: emd_60944.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.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.21343549 - 0.4619113
Average (Standard dev.)0.0010263855 (±0.014508023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60944_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_60944_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 : Lactobacillus casei DdmE bound with guide and target

EntireName: Lactobacillus casei DdmE bound with guide and target
Components
  • Complex: Lactobacillus casei DdmE bound with guide and target
    • DNA: DNA (25-MER)
    • DNA: DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')
    • DNA: DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3')
    • Protein or peptide: DdmE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Lactobacillus casei DdmE bound with guide and target

SupramoleculeName: Lactobacillus casei DdmE bound with guide and target / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lacticaseibacillus (bacteria)

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Macromolecule #1: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 7.706998 KDa
SequenceString:
(DA)(DG)(DA)(DT)(DT)(DA)(DG)(DA)(DG)(DC) (DC)(DG)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DT) (DC)(DA)(DA)(DG)(DT)

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Macromolecule #2: DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')

MacromoleculeName: DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 4.559971 KDa
SequenceString:
(DT)(DG)(DA)(DC)(DG)(DG)(DC)(DT)(DC)(DT) (DA)(DA)(DT)(DC)(DT)

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Macromolecule #3: DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3')

MacromoleculeName: DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 3.333198 KDa
SequenceString:
(DC)(DT)(DT)(DG)(DA)(DT)(DA)(DC)(DG)(DA) (DC)

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Macromolecule #4: DdmE

MacromoleculeName: DdmE / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 83.294773 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEQQSMIRTT RLDYKINMMQ LQADFKFLVV KIIDRSAFKD YNKLLASWSP EAVTSIRGRY KKGDYLMMFR QLPAIPTIAG LELHEILLE DMGEFKIYPN HLLQLLLNQQ SANEKSLLEP CKTPELLISG EEWYREFRDM RQQYYALKLK VNWQQDLEMS V QTFTQVTE ...String:
MEQQSMIRTT RLDYKINMMQ LQADFKFLVV KIIDRSAFKD YNKLLASWSP EAVTSIRGRY KKGDYLMMFR QLPAIPTIAG LELHEILLE DMGEFKIYPN HLLQLLLNQQ SANEKSLLEP CKTPELLISG EEWYREFRDM RQQYYALKLK VNWQQDLEMS V QTFTQVTE FQWDKQIYQF DEKRGRFQLC YQPSPGIYFV QGNHSANRNY IDFLSLQNKS SFYKSKVGVV QLVLDNLNLN AE KYLLRPV TFHKSLVEHS SRLKLSKRET IWQQLAGSSL NIYAQVNDRL SQELADQLAD HLIRSQLVRK NSVHVVRSQK IQS GFNIQV IRDVRGRAAE DGYEVAKNDQ IVQHLTVENF GHYQEGDKEI TWKPKVSGKH HDPARDVAIV KLIQELCIKR DLAN GKLKT VEPKLASLTQ PLEFYYFAFL KKSFDPEVMV IKLAFTPEME LRFSKKKVRL NALTSDDEYT QVCKRVFDSL AAPKF YSAW DSVDCVVRSG NKQLLIQRLN RTIMPDGKQI RKQLELNRPD KTLWRDKVVE ELGELRPMVS GDSDYVAAYE QLQALV TGM RPSFPLKDLD EAARKAGLNP KRRDMRQVNQ FLTENATFTL KTTLQRELPD SPLAGMKWIG LTRIEEGEGH FNTFYFV GS DKSLKPVVNR AVTLRRLLPL AGDAGIIDEL FPKLAAMMSV EFVRSGQYTV VPYPVKYLRE YWYSILRQHP EYR

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18580
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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