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- EMDB-36621: Cryo-EM structure of a DNA-protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36621
TitleCryo-EM structure of a DNA-protein complex
Map data
Sample
  • Complex: a DNA-protein complex
    • Protein or peptide: Argonaute family protein
    • DNA: DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*C)-3')
    • DNA: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsDNA / protein / interaction / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / Argonaute, N-terminal domain / Argonaute PAZ domain, archaea / PAZ domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. ...: / Argonaute, N-terminal domain / Argonaute PAZ domain, archaea / PAZ domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. / PAZ domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Argonaute family protein
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of a DNA-protein complex
Authors: Li Z
History
DepositionJun 20, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36621.png

Downloads & links

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Map

FileDownload / File: emd_36621.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
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 240 pix.
= 204. Å		0.85 Å/pix.
x 240 pix.
= 204. Å		0.85 Å/pix.
x 240 pix.
= 204. 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: 0.4
Minimum - Maximum-1.7050296 - 3.272998
Average (Standard dev.)0.00036209356 (±0.111459404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36621_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_36621_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 : a DNA-protein complex

EntireName: a DNA-protein complex
Components
  • Complex: a DNA-protein complex
    • Protein or peptide: Argonaute family protein
    • DNA: DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*C)-3')
    • DNA: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: a DNA-protein complex

SupramoleculeName: a DNA-protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermococcus thioreducens (archaea)

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Macromolecule #1: Argonaute family protein

MacromoleculeName: Argonaute family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus thioreducens (archaea)
Molecular weightTheoretical: 87.488398 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLMKVLTNMV KLNQDIIPNE IYLYKIFNKP EDGMNIYKIA YRNHGIVIDP QNRIIATPSE LEYSGKFAIE DEISFNELPE NYQNRLVLR ILRDNGISDH ALSRTLQKYR KPKPFGDFEV IPEIRSSVIK HGGDFYLVLH LSHQIRSKKT LWELVGRNKD A LRDFLKEH ...String:
MLMKVLTNMV KLNQDIIPNE IYLYKIFNKP EDGMNIYKIA YRNHGIVIDP QNRIIATPSE LEYSGKFAIE DEISFNELPE NYQNRLVLR ILRDNGISDH ALSRTLQKYR KPKPFGDFEV IPEIRSSVIK HGGDFYLVLH LSHQIRSKKT LWELVGRNKD A LRDFLKEH RGTILLRDIA SEHKVVYKPI FKRYNGDPDL IEDNSNDVEH WYDYHLERYW NTPELKKEFY KKFGPVDLNQ PI ILAKPLR QHNRGDLVHL LPQFVVPVYN AEQLNDILAS EILEYLKLTS NQRISLLSRL INDIKTNTNI IVSSLTELEA NTF DVDLND MLQVRNADNV KVTLSELEIS KTRLFTWMKS RKYPVILPYD IPQKLKKIEK IPVFIIVDSA LSRDIQTFAK DEFR YLISS LQKSLSNWVD FPILDIRDKY IFTIDLTSDK DIVNLSIKLV NLMKNAELGL ALIATRTKLP NETFDEVKKR LFSVN IISQ VVNEATLYKR DKYNESRLNL YVQHNLLFQI LSKLGIKYYV LRHKFSYDYI VGIDVTPMKL SHGYIGGSAV MFDSQG YIR KIIPVEIGEQ MGESIDMKEF FKDMVVQFGK FGIDLEGKSI LILRDGKITK DEEEGLAYIS KVFGIKITTF NIVKRHL LR IFANRKLYLR LANSVYLLPH RIKQSVGTPV PLKLSEKRLI LDGTITSQEI TYNDIFEILL LSELNYGSIS ADMKLPAP V HYAHKFVRAL RKGWRIREEL LAEGFLYFV

UniProtKB: Argonaute family protein

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

MacromoleculeName: DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*C)-3')
type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Thermococcus thioreducens (archaea)
Molecular weightTheoretical: 4.747109 KDa
SequenceString:
(DA)(DC)(DA)(DA)(DC)(DC)(DT)(DA)(DC)(DT) (DA)(DC)(DC)(DT)(DC)(DC)

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

MacromoleculeName: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Thermococcus thioreducens (archaea)
Molecular weightTheoretical: 5.049273 KDa
SequenceString:
(DG)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA) (DG)(DG)(DT)(DT)(DG)(DT)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / 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

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

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 629194
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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