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- EMDB-38373: protein-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38373
Titleprotein-DNA complex
Map data
Sample
  • Complex: protein-DNA complex
    • Protein or peptide: Piwi domain-containing protein
    • DNA: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3')
    • DNA: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*AP*TP*TP*TP*GP*T)-3')
    • DNA: DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3')
  • Ligand: MAGNESIUM ION
KeywordsDNA / protein / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homologyRibonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / Piwi domain-containing protein
Function and homology information
Biological speciesMucilaginibacter paludis DSM 18603 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhuang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: protein-DNA complex
Authors: Zhuang L
History
DepositionDec 19, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38373.png

Downloads & links

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Map

FileDownload / File: emd_38373.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 220 pix.
= 187. Å		0.85 Å/pix.
x 220 pix.
= 187. Å		0.85 Å/pix.
x 220 pix.
= 187. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.045004312 - 0.09983504
Average (Standard dev.)0.000258176 (±0.002890168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 187.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38373_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_38373_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 : protein-DNA complex

EntireName: protein-DNA complex
Components
  • Complex: protein-DNA complex
    • Protein or peptide: Piwi domain-containing protein
    • DNA: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3')
    • DNA: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*AP*TP*TP*TP*GP*T)-3')
    • DNA: DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: protein-DNA complex

SupramoleculeName: protein-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)

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Macromolecule #1: Piwi domain-containing protein

MacromoleculeName: Piwi domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)
Molecular weightTheoretical: 91.915383 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKDHILNLYR IDNLSELDFS YKLIDFDLSF IAGKEELLNK QLQKIAEEVS SVTKGPTAVL KRNQRFFVAV PADKQMEDRS IDGIPFSIP IKLLPEVYRI DSKDIQGHQL DVVYKFLDYE IRRQLGQHRD LWKLNTHQFF LREPMKGIQG SINVFEGFTY K LARLADGH ...String:
MKDHILNLYR IDNLSELDFS YKLIDFDLSF IAGKEELLNK QLQKIAEEVS SVTKGPTAVL KRNQRFFVAV PADKQMEDRS IDGIPFSIP IKLLPEVYRI DSKDIQGHQL DVVYKFLDYE IRRQLGQHRD LWKLNTHQFF LREPMKGIQG SINVFEGFTY K LARLADGH FYVTLDLSTK YIDKYCLSHY INEGNVRTFE NNYKGRRFLY LNGDNWYTIE LLGFGKSVKE QDFIREGTTY NV LNYITEK IEHSRTDLKR YVKPNDLSMS YTYPGRTMDP HSGATSLARM LYNTKDERVK SLHYLSIKGP SKRFEAINNY ISS YFKNLK FNAGKLLISN EPLVEKIKNF WIPELLFNNN RRLKITGFNS GMRDFAYQRK QLIKNNGVLN RTSFDVQYLL VPDE QYMDA NLVEGFKNNA EFLIKKLAPA FDKFIIIRYP VKSCTSASVQ IQEIEKVLHR RNALHGFALV VLPDLDAFSP AFLKT FHEL LKSKFYPDLK VQCASAHNIS SFFKPFSTAG NNGIVEYRVV EALKGRFSSY LFYLVLEHLI VNRKWPYALA KNLFYD IYI GIDVHDRHAG FTFFFKNGEQ IIFHPEEVPQ KTNSQRVEKV RAKTLNKVIY EKLKLYIPLF APNPNGIVIV RDGRSFG VE YKALQAAINT LAAEGIVNKD TVKYGVVDLH KQSSVPIRIA AKTNSYDQLE NPVAGSYKLV SPKEGFIFST GYPFDIKG T SRPLNLSMKE GDLDFMKVME DVFCQIMLAF SAPDKSNFLP VIIKLIDTLL EPLTATRETA DEAEEDEEEM MDIN

UniProtKB: Piwi domain-containing protein

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Macromolecule #2: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)
Molecular weightTheoretical: 2.490666 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DG)(DT)(DA)(DA)

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

MacromoleculeName: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*AP*TP*TP*TP*GP*T)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)
Molecular weightTheoretical: 5.02426 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA) (DG)(DG)(DT)(DT)(DG)(DT)

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Macromolecule #4: DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)
Molecular weightTheoretical: 2.138476 KDa
SequenceString:
(DA)(DT)(DA)(DA)(DA)(DA)(DA)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274970
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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