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- EMDB-80550: Cryo-EM structure of the hexameric DRT3b complex -

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Basic information

Entry
Database: EMDB / ID: EMD-80550
TitleCryo-EM structure of the hexameric DRT3b complex
Map dataCryoSPARC sharpened and FSC weighted
Sample
  • Complex: Cryo-EM structure of the hexameric EcoDRT3b complex
    • Protein or peptide: Small ubiquitin-related modifier,RNA-directed DNA polymerase
    • DNA: DNA
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRNA independent DNA polymerase / protein-primed DNA polymerase / DNA BINDING PROTEIN
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / protein tag activity / identical protein binding / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Small ubiquitin-related modifier
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYoneyama K / Nagahata N / Hiraizumi M / Yamashita K / Nishimasu H
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
Japan Society for the Promotion of Science (JSPS)25H00436 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of the hexameric DRT3b complex
Authors: Yoneyama K
History
DepositionApr 27, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_80550.png

Downloads & links

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Map

FileDownload / File: emd_80550.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC sharpened and FSC weighted
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.29680273 - 0.4815241
Average (Standard dev.)0.00089437596 (±0.017550047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80550_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80550_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_80550_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 : Cryo-EM structure of the hexameric EcoDRT3b complex

EntireName: Cryo-EM structure of the hexameric EcoDRT3b complex
Components
  • Complex: Cryo-EM structure of the hexameric EcoDRT3b complex
    • Protein or peptide: Small ubiquitin-related modifier,RNA-directed DNA polymerase
    • DNA: DNA
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the hexameric EcoDRT3b complex

SupramoleculeName: Cryo-EM structure of the hexameric EcoDRT3b complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Small ubiquitin-related modifier,RNA-directed DNA polymerase

MacromoleculeName: Small ubiquitin-related modifier,RNA-directed DNA polymerase
type: protein_or_peptide / ID: 1 / Details: SUMO tag,SUMO tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 90.781156 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHGS LQDSEVNQEA KPEVKPEVKP ETHINLKVSD GSSEIFFKIK KTTPLRRLME AFAKRQGKEM DSLRFLYDGI RIQADQAPE DLDMEDNDII EAHREQIGGM KIKISKSDYK RVLLTDILPY EVPILFSNEG FYKLISENKV LPGTFSEGLK L DSYTIPYS ...String:
MGHHHHHHGS LQDSEVNQEA KPEVKPEVKP ETHINLKVSD GSSEIFFKIK KTTPLRRLME AFAKRQGKEM DSLRFLYDGI RIQADQAPE DLDMEDNDII EAHREQIGGM KIKISKSDYK RVLLTDILPY EVPILFSNEG FYKLISENKV LPGTFSEGLK L DSYTIPYS YKIKKGLASS RSLGIIHPST QLRICDFYDK YEHLMVHMCT KSPFSLRYPS KIGSYYYEKD FLKSRINLKD GL VQFHNHG FDSQETSSSS HFSYKKYPFI YKFYESYEFH RLERKFRKLL KLDIAKCFSH IYTHSVSWAV KSKEFSKVNR TYN SFEGCL DKLFQDANYG ETNGIIIGPE FSRIFAEIIL QRVDLNVESH LNLEPGIVKD KSYAIRRYVD DYFIFADDDE TFKL IEFVL ANELEKYKLY LNESKKEFIE RPFVTGATMA KNDIAEIIED LYGSLIHTEK LDELTAMVNL NPDVKIQPEN MNDLF PLKG VWNKKLHADK FIKRIKIAVR KNNTTFDLVS SYLLSAIKSK FFKVIRLLRM FDLSGKEDIT YKFFSIFNEV IFFIYA MDF RVRQTYIISQ VILEINSFAN KQASDISEVI KKNTFDELLM CMKSMGNIHE RPVELSNLLI CMKGLGEQYK LNPDEFK DL LGISENECFY DLEYFSICSM LHYIGDDVLY LKMKEDIVLA IQSLISGRND IKKDTETFML FLDMMTCPYL TVKHKRII Y RTYVEANTGQ KRFTNAVIDS EIDSLKNNVI FFNWSGDADL EHVLYKKELR TAYE

UniProtKB: Small ubiquitin-related modifier

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Macromolecule #2: DNA

MacromoleculeName: DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 4.171763 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DC)(DA)

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
Details: 20 mM HEPES-NaOH, 300 mM NaCl, 5 mM MgCl2, and 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec.
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: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 13084
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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