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- EMDB-63396: cryo-EM structure of E.coli DRT4 mutant with D240A and D241A. -

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Basic information

Entry
Database: EMDB / ID: EMD-63396
Titlecryo-EM structure of E.coli DRT4 mutant with D240A and D241A.
Map data
Sample
  • Complex: DRT4 homohexamer
    • Protein or peptide: Reverse transcriptase domain-containing protein
Keywordsanti-phage defense / DNA BINDING PROTEIN
Function / homologyReverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYan XH / Jin XH / Guan ZY / Zou TT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: DRT4 executes RNA cleavage for anti-phage defense
Authors: Yan XH / Zou TT
History
DepositionFeb 8, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63396.png

Downloads & links

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Map

FileDownload / File: emd_63396.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.)
0.84 Å/pix.
x 240 pix.
= 201.6 Å		0.84 Å/pix.
x 240 pix.
= 201.6 Å		0.84 Å/pix.
x 240 pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.0319346 - 1.7226895
Average (Standard dev.)0.008499285 (±0.08552417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 201.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63396_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_63396_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 : DRT4 homohexamer

EntireName: DRT4 homohexamer
Components
  • Complex: DRT4 homohexamer
    • Protein or peptide: Reverse transcriptase domain-containing protein

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Supramolecule #1: DRT4 homohexamer

SupramoleculeName: DRT4 homohexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Reverse transcriptase domain-containing protein

MacromoleculeName: Reverse transcriptase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64.110406 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVIFDEKRHL YEALLRHNYF PNQKGSISEI PPCFSSRTFT PEIAELISSD TSGRRSLQGY DCVEYYATRY NNFPRTLSII HPKAYSKLA KHIHDNWEEI RFIKENENSM IKPDMHADGR IIIMNYEDAE TKTIRELNDG FGRRFKVNAD ISGCFTNIYS H SIPWAVIG ...String:
MVIFDEKRHL YEALLRHNYF PNQKGSISEI PPCFSSRTFT PEIAELISSD TSGRRSLQGY DCVEYYATRY NNFPRTLSII HPKAYSKLA KHIHDNWEEI RFIKENENSM IKPDMHADGR IIIMNYEDAE TKTIRELNDG FGRRFKVNAD ISGCFTNIYS H SIPWAVIG VNNAKIALNT KVKNQDKHWS DKLDYFQRQA KRNETHGVPI GPATSSIVCE IILSAVDKRL RDDGFLFRRY IA AYTCYCK THDDAKEFLH LLGMELSKYK LSLNLHKTKI TNLPGTLNDN WVSLLNVNSP TKKRFTDQDL NKLSSSEVIN FLD YAVQLN TQVGGGSILK YAISLVINNL DEYTITQVYD YLLNLSWHYP MLIPYLGVLI EHVYLDDGDE YKNKFNEILS MCAE NKCSD GMAWTLYFCI KNNIDIDDDV IEKIICFGDC LSLCLLDSSD IYEEKINNFV SDIIKLDYEY DIDRYWLLFY QRFFK DKAP SPYNDKCFDI MKGYGVDFMP DENYKTKAES YCHVVNNPFL EDGDEIVSFN DYMAIALEHH HHHHHH

UniProtKB: Reverse transcriptase domain-containing protein

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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: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91579
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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