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- EMDB-36047: Structure of the SPARTA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36047
TitleStructure of the SPARTA complex
Map data
Sample
  • Complex: SPARTA complex
    • Protein or peptide: Piwi domain-containing protein
    • Protein or peptide: TIR domain-containing protein
    • RNA: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')
    • DNA: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')
Keywordscomplex / immune / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA-DNA complex
Function / homology
Function and homology information


nucleic acid binding / signal transduction
Similarity search - Function
TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Piwi domain-containing protein / TIR domain-containing protein
Similarity search - Component
Biological speciesMaribacter polysiphoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsGuo M / Zhu Y / Lin Z / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31825008, 31422014, U21A20276, China
CitationJournal: Cell Res / Year: 2023
Title: Cryo-EM structure of the ssDNA-activated SPARTA complex.
Authors: Minghui Guo / Yuwei Zhu / Zhiying Lin / Dehui Yang / Anqi Zhang / Changyou Guo / Zhiwei Huang /
History
DepositionApr 28, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36047.png

Downloads & links

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Map

FileDownload / File: emd_36047.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0773 Å
Density
Contour LevelBy AUTHOR: 0.286
Minimum - Maximum-0.64374155 - 1.5508344
Average (Standard dev.)-0.0007770178 (±0.036290985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36047_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_36047_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 : SPARTA complex

EntireName: SPARTA complex
Components
  • Complex: SPARTA complex
    • Protein or peptide: Piwi domain-containing protein
    • Protein or peptide: TIR domain-containing protein
    • RNA: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')
    • DNA: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')

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Supramolecule #1: SPARTA complex

SupramoleculeName: SPARTA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Maribacter polysiphoniae (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: 4 / Enantiomer: LEVO
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Molecular weightTheoretical: 57.978254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKELIYIEEP KILFAHGQKC TDARDGLALF GPLNNLYGIK SGVIGTKQGL KIFRDYLDHI QKPIYNSNSI TRPMFPGFEA VFDCKWEST GITFKEVTNE DIGKFLYNSS THKRTYDLVS LFIDKIISAN KNEDENVDVW FVIVPDEIYK YCRPNSVLPK E MVQTKALM ...String:
MKELIYIEEP KILFAHGQKC TDARDGLALF GPLNNLYGIK SGVIGTKQGL KIFRDYLDHI QKPIYNSNSI TRPMFPGFEA VFDCKWEST GITFKEVTNE DIGKFLYNSS THKRTYDLVS LFIDKIISAN KNEDENVDVW FVIVPDEIYK YCRPNSVLPK E MVQTKALM SKSKAKSFRY EPSLFPDINI ELKEQEKEAE TYNYDAQFHD QFKARLLKHT IPTQIFREST LAWRDFKNAF GL PIRDFSK IEGHLAWTIS TAAFYKAGGK PWKLSDVRNG VCYLGLVYKK VEKSKNPRNA CCAAQMFLDN GDGTVFKGEV GPW YNPKNG QYHLEPKEAK ALLSQSLQSY KEQIGEYPKE VFIHAKTRFN HQEWDAFLEV TPKETNLVGV TISKTKPLKL YKTE GDYTI LRGNAYVVNE RSAFLWTVGY VPKIQTALSM EVPNPLFIEI NKGEADIKQV LKDILSLTKL NYNACIFADG EPVTL RFAD KIGEILTAST DIKTPPLAFK YY

UniProtKB: Piwi domain-containing protein

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Macromolecule #2: TIR domain-containing protein

MacromoleculeName: TIR domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Molecular weightTheoretical: 49.39659 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRNKIFISHA TPDDNDFTRW LALKLIGLGY EVWCDILFLD KGVDFWSNIE KVIREDTCKF LLVSSSYSNQ REGVLKELAV AAKVKKQLK DDKFIIPLAI DEQLSYDDIN IDIVRLNAID FKMSWARGLK DILEAFEKQK VPKEVADASK SNLLYQQIFL H DKSVIEKE ...String:
MRNKIFISHA TPDDNDFTRW LALKLIGLGY EVWCDILFLD KGVDFWSNIE KVIREDTCKF LLVSSSYSNQ REGVLKELAV AAKVKKQLK DDKFIIPLAI DEQLSYDDIN IDIVRLNAID FKMSWARGLK DILEAFEKQK VPKEVADASK SNLLYQQIFL H DKSVIEKE EIYDSNWLSI LSFPEELRFH EYNWMLPKRF DVRELTFPAV RYKNYLCTFA WAYDFTYHLP KTETYHKSKT IR IPTEEIL SGSYDSNFIR NAECKRLIVQ LLNKAFELRM KDKEVQEYEM SNKTAYWLEK GKLEKDKFEK TMLVGKQKDK NWH FAISGA SKLYPFPVLM ISSHIFFTAD GKKLIDSSSV QHSSRRRQGK NWWNNTWRTK LLAFIKYLSD DDTSFYLEMG SEEK VFVSN EPVKFKGNVS YNI

UniProtKB: TIR domain-containing protein

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Macromolecule #3: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP...

MacromoleculeName: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3')
type: rna / ID: 3 / Number of copies: 4
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Molecular weightTheoretical: 6.000577 KDa
SequenceString:
UGACGGCUCU AAUCUAUUA

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Macromolecule #4: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP...

MacromoleculeName: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3')
type: dna / ID: 4 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Maribacter polysiphoniae (bacteria)
Molecular weightTheoretical: 7.425842 KDa
SequenceString:
(DT)(DA)(DA)(DT)(DA)(DG)(DA)(DT)(DT)(DA) (DG)(DA)(DG)(DC)(DC)(DG)(DT)(DC)(DA)(DA) (DT)(DA)(DG)(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: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 832006

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