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- EMDB-31829: Cryo-EM structure of E.coli retron-Ec86 in complex with its effec... -

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Basic information

Entry
Database: EMDB / ID: EMD-31829
TitleCryo-EM structure of E.coli retron-Ec86 in complex with its effector at 2.8 angstrom
Map data
Sample
  • Complex: retron-Ec86 (RT-msDNA-RNA)
    • Protein or peptide: RNA-directed DNA polymerase from retron EC86Reverse transcriptase
    • Protein or peptide: retron St85 family effector protein
    • DNA: DNA (105-MER)
    • RNA: RNA (81-MER)
    • RNA: RNA (14-MER)
Function / homology
Function and homology information


RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / defense response to virus / RNA binding / metal ion binding
Similarity search - Function
RNA-directed DNA polymerase (reverse transcriptase), msDNA / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / Retron Ec86 reverse transcriptase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsWang YJ / Guan ZY / Zou TT
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0507700 China
National Natural Science Foundation of China (NSFC)32070174 China
CitationJournal: To Be Published
Title: Structural insight into anti-phage Retron-Ec86 complex
Authors: Wang TJ / Guan ZY / Zou TT
History
DepositionAug 27, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31829.png

Downloads & links

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Map

FileDownload / File: emd_31829.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.295011 - 2.7605934
Average (Standard dev.)0.005189105 (±0.07092702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : retron-Ec86 (RT-msDNA-RNA)

EntireName: retron-Ec86 (RT-msDNA-RNA)
Components
  • Complex: retron-Ec86 (RT-msDNA-RNA)
    • Protein or peptide: RNA-directed DNA polymerase from retron EC86Reverse transcriptase
    • Protein or peptide: retron St85 family effector protein
    • DNA: DNA (105-MER)
    • RNA: RNA (81-MER)
    • RNA: RNA (14-MER)

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Supramolecule #1: retron-Ec86 (RT-msDNA-RNA)

SupramoleculeName: retron-Ec86 (RT-msDNA-RNA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: RNA-directed DNA polymerase from retron EC86

MacromoleculeName: RNA-directed DNA polymerase from retron EC86 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 37.83207 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKSAEYLNTF RLRNLGLPVM NNLHDMSKAT RISVETLRLL IYTADFRYRI YTVEKKGPEK RMRTIYQPSR ELKALQGWVL RNILDKLSS SPFSIGFEKH QSILNNATPH IGANFILNID LEDFFPSLTA NKVFGVFHSL GYNRLISSVL TKICCYKNLL P QGAPSSPK ...String:
MKSAEYLNTF RLRNLGLPVM NNLHDMSKAT RISVETLRLL IYTADFRYRI YTVEKKGPEK RMRTIYQPSR ELKALQGWVL RNILDKLSS SPFSIGFEKH QSILNNATPH IGANFILNID LEDFFPSLTA NKVFGVFHSL GYNRLISSVL TKICCYKNLL P QGAPSSPK LANLICSKLD YRIQGYAGSR GLIYTRYADD LTLSAQSMKK VVKARDFLFS IIPSEGLVIN SKKTCISGPR SQ RKVTGLV ISQEKVGIGR EKYKEIRAKI HHIFCGKSSE IEHVRGWLSF ILSVDSKSHR RLITYISKLE KKYGKNPLNK AKT LEHHHH HHHH

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Macromolecule #2: retron St85 family effector protein

MacromoleculeName: retron St85 family effector protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.538242 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNKKFTDEQQ QQLIGHLTKK GFYRGANIKI TIFLCGGDVA NHQSWRHQLS QFLAKFSDVD IFYPEDLFDD LLAGQGQHSL LSLENILAE AVDVIILFPE SPGSFTELGA FSNNENLRRK LICIQDAKFK SKRSFINYGP VRLLRKFNSK SVLRCSSNEL K EMCDSSID ...String:
MNKKFTDEQQ QQLIGHLTKK GFYRGANIKI TIFLCGGDVA NHQSWRHQLS QFLAKFSDVD IFYPEDLFDD LLAGQGQHSL LSLENILAE AVDVIILFPE SPGSFTELGA FSNNENLRRK LICIQDAKFK SKRSFINYGP VRLLRKFNSK SVLRCSSNEL K EMCDSSID VARKLRLYKK LMASIKKVRK ENKVSKDIGN ILYAERFLLP CIYLLDSVNY RTLCELAFKA IKQDDVLSKI IV RSVVSRL INERKILQMT DGYQVTALGA SYVRSVFDRK TLDRLRLEIM NFENRRKSTF NYDKIPYAHP

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Macromolecule #3: DNA (105-MER)

MacromoleculeName: DNA (105-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 32.468803 KDa
SequenceString: (DG)(DA)(DA)(DA)(DG)(DT)(DT)(DG)(DC)(DG) (DC)(DA)(DC)(DC)(DC)(DT)(DT)(DA)(DC)(DG) (DT)(DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA) (DA)(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DC)(DC) (DT) (DG)(DG)(DT)(DT)(DG)(DG) ...String:
(DG)(DA)(DA)(DA)(DG)(DT)(DT)(DG)(DC)(DG) (DC)(DA)(DC)(DC)(DC)(DT)(DT)(DA)(DC)(DG) (DT)(DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA) (DA)(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DC)(DC) (DT) (DG)(DG)(DT)(DT)(DG)(DG)(DC)(DT) (DC)(DG)(DG)(DA)(DG)(DA)(DG)(DC)(DA)(DT) (DC)(DA) (DG)(DG)(DC)(DG)(DA)(DT)(DG) (DC)(DT)(DC)(DT)(DC)(DC)(DG)(DT)(DT)(DC) (DC)(DA)(DA) (DC)(DA)(DA)(DG)(DG)(DA) (DA)(DA)(DA)(DC)(DA)(DG)(DA)(DC)(DA)(DG) (DT)(DA)(DA)(DC) (DT)(DC)(DA)(DG)(DA)

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Macromolecule #4: RNA (81-MER)

MacromoleculeName: RNA (81-MER) / type: rna / ID: 4 / Number of copies: 2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.870203 KDa
SequenceString:
UGCGCACCCU UAGCGAGAGG UUUAUCAUUA AGGUCAACCU CUGGAUGUUG UUUCGGCAUC CUGCAUUGAA UCUGAGUUAC U

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Macromolecule #5: RNA (14-MER)

MacromoleculeName: RNA (14-MER) / type: rna / ID: 5 / Number of copies: 2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 4.541771 KDa
SequenceString:
CGUAAGGGUG CGCA

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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

Concentration0.4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.68 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137409

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