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- EMDB-72883: Defense-associated reverse transcriptase 1 (DRT1) filament -

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Basic information

Entry
Database: EMDB / ID: EMD-72883
TitleDefense-associated reverse transcriptase 1 (DRT1) filament
Map data
Sample
  • Complex: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
    • Protein or peptide: Defense-associated reverse transcriptase 1
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAnti-phage defense / DNA synthesis / Nitrilase domain / RT domain / filament / ANTIVIRAL PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJohnson NV / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Semirandom DNA adducts regulate a filamentous defense-associated reverse transcriptase
Authors: Neville N / Johnson NV / Escobar EE / Chiang CH / Nreca A / Johnson SR / Dai N / Hanneman A / Correa Jr IR / McLellan JS / Trachman III RJ
History
DepositionSep 25, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72883.png

Downloads & links

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Map

FileDownload / File: emd_72883.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.07320925 - 1.9622343
Average (Standard dev.)0.006095051 (±0.053148303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_72883_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72883_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72883_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 : DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain

EntireName: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
Components
  • Complex: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
    • Protein or peptide: Defense-associated reverse transcriptase 1
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain

SupramoleculeName: DRT1 bound 1:1 to dATP with 2 coordinated Mg2+ ions per chain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 565 kDa/nm

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Macromolecule #1: Defense-associated reverse transcriptase 1

MacromoleculeName: Defense-associated reverse transcriptase 1 / type: protein_or_peptide / ID: 1 / Details: DRT1 reacted with dNTPs / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 141.551984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLLNKKYYN LEPNFDYLKD SFILGLAWKK TDRFVRTHNW YADLLALDKC AFDISDEVTS WSSEAVNRNL SKSDIELIPA PKRASWFFN KGKWTTNKDD RKLRPLANIS IKDQSFATAV TMCLADAIET RQKDCSLRNL GYAEHVNKKV VSYGNRLVCD W DNERARFR ...String:
MKLLNKKYYN LEPNFDYLKD SFILGLAWKK TDRFVRTHNW YADLLALDKC AFDISDEVTS WSSEAVNRNL SKSDIELIPA PKRASWFFN KGKWTTNKDD RKLRPLANIS IKDQSFATAV TMCLADAIET RQKDCSLRNL GYAEHVNKKV VSYGNRLVCD W DNERARFR WGGSEYYRKF STDYRNFLQR PVYIGRETVN KISEIDDVYI ISLDLKNFFG SIKISTLLEK LKKISSDHYD HN IINENEF WGLASQILNW EWPEDSLSLL KNLDIEEENV GLPQGLASAG ALANAYLIEF DESLTSNLRT KIDGSQIVLH DYC RYVDDI RLVISGEALT NEEIKKSIHE LVQRILDETL DQDESDNEPY LKINDKKTYI LGLSDIDNGS SLTNRINEIQ NEVG TSSIP ERNGLDNNIP ALQQLLLTEQ DNFLEDADGL FSGFNNDKSI KLESLRRFSA HRLETSLANK SKLISPAERK QFDNE SALI AKKLLKTWLK DPSIMVIFRK AITINPNLDA YKTILEIIFL RIQHNREKCD RYIMLYLLSD IFRSVVDIYR KLSPEC TSD YQKLMSEVTS FAHKLLSCRS VIPNYAYQQA LFYLAVINKP FIASKKSSSD LSKLQHVLIK RHLEPLSSSD GYLFELS AQ ISKDYQANVA FLLSHTNTTE VVDSIVEKFA YRGGEFWNSI WKEFVRTKDK VRINKFRWAI PKNESKPNGS DHYLSSVI S FKENPFKYEH ALLKLGIALV NLLEDTEKNV WQSDGKQYSP HEIKVKLEGH STSWTELWRQ NSIISCSIDK IAQDPRYES PKWLVNCQQA KNDEKKIYWV CSVLRSAALG NVDYTQRNDL KPDRVEYDGI HSQFYKRRMG MLHTPESIVG SYATITDWFA SFLQHGLQW PGFSSSYINQ EDILSITSLG EFKKCLLERL GYLNTQICTS SSVPTLPTVV NRPELASNYF RIVTVQQLFP K DKHFHPSD VTLDNPEVRW KHREHLAEIC KLTEQTLDAK LKTESRDHTS TADLIVFSEL AVHPEDEDIV RALAFRTRSI IF CGFVFCE QDGQIVNKAR WIIPDSSESG TQWRVRDQGK FHMTSGEMSL GVHGYRPSQH IISIEGHTEG PFKLTGAICY DAT DIKLAA DLRDLTDMFV IAAYNKDVDT FDNMASALQW HMYQHVIITN TGEYGGSTMQ APYKEKHHKL ISHAHGTGQI AIST ADIDL AAFRRKIKEY KKTKTQPAGF KRKH

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Macromolecule #2: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 16 / 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 statefilament

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AF2 model of a DRT1 tetramer
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140634
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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