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- EMDB-64991: Cryo-EM structure of the hexameric DRT4 -

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Basic information

Entry
Database: EMDB / ID: EMD-64991
TitleCryo-EM structure of the hexameric DRT4
Map data
Sample
  • Complex: DRT4-DNA
    • Protein or peptide: Reverse transcriptase domain-containing protein
    • DNA: DNA (5'-D(P*CP*CP*CP*AP*A)-3')
KeywordsUG15 / DRT4 / Reverse transcriptases / UG/Abi system / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homologyReverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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: 2.27 Å
AuthorsWang Y / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the hexameric DRT4
Authors: Wang Y / Deng Z
History
DepositionJun 9, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64991.png

Downloads & links

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Map

FileDownload / File: emd_64991.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.8584385 - 2.749706
Average (Standard dev.)0.0003112736 (±0.096939646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64991_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_64991_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-DNA

EntireName: DRT4-DNA
Components
  • Complex: DRT4-DNA
    • Protein or peptide: Reverse transcriptase domain-containing protein
    • DNA: DNA (5'-D(P*CP*CP*CP*AP*A)-3')

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Supramolecule #1: DRT4-DNA

SupramoleculeName: DRT4-DNA / 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: 63.911047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGM VIFDEKRHLY EALLRHNYFP NQKGSISEIP PCFSSRTFTP EIAELISSDT SGRRSLQGYD CVEYYATRYN NFPRTLSII HPKAYSKLAK HIHDNWEEIR FIKENENSMI KPDMHADGRI IIMNYEDAET KTIRELNDGF GRRFKVNADI S GCFTNIYS ...String:
HHHHHHSSGM VIFDEKRHLY EALLRHNYFP NQKGSISEIP PCFSSRTFTP EIAELISSDT SGRRSLQGYD CVEYYATRYN NFPRTLSII HPKAYSKLAK HIHDNWEEIR FIKENENSMI KPDMHADGRI IIMNYEDAET KTIRELNDGF GRRFKVNADI S GCFTNIYS HSIPWAVIGV NNAKIALNTK VKNQDKHWSD KLDYFQRQAK RNETHGVPIG PATSSIVCEI ILSAVDKRLR DD GFLFRRY IDDYTCYCKT HDDAKEFLHL LGMELSKYKL SLNLHKTKIT NLPGTLNDNW VSLLNVNSPT KKRFTDQDLN KLS SSEVIN FLDYAVQLNT QVGGGSILKY AISLVINNLD EYTITQVYDY LLNLSWHYPM LIPYLGVLIE HVYLDDGDEY KNKF NEILS MCAENKCSDG MAWTLYFCIK NNIDIDDDVI EKIICFGDCL SLCLLDSSDI YEEKINNFVS DIIKLDYEYD IDRYW LLFY QRFFKDKAPS PYNDKCFDIM KGYGVDFMPD ENYKTKAESY CHVVNNPFLE DGDEIVSFND YMAIA

UniProtKB: Reverse transcriptase domain-containing protein

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

MacromoleculeName: DNA (5'-D(P*CP*CP*CP*AP*A)-3') / type: dna / ID: 2 / Number of copies: 6 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.449002 KDa
SequenceString:
(DC)(DC)(DC)(DA)(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: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 306468
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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