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- PDB-26cz: Cryo-EM structure of the hexameric DRT3b complex -

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Basic information

Entry
Database: PDB / ID: 26cz
TitleCryo-EM structure of the hexameric DRT3b complex
Components
  • DNA
  • Small ubiquitin-related modifier,RNA-directed DNA polymerase
KeywordsDNA BINDING PROTEIN / RNA independent DNA polymerase / protein-primed DNA polymerase
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
DNA / DNA (> 10) / Small ubiquitin-related modifier
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYoneyama, K. / Nagahata, N. / Hiraizumi, M. / Yamashita, K. / Nishimasu, H.
Funding support Japan, 2items
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, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small ubiquitin-related modifier,RNA-directed DNA polymerase
B: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9773
Polymers94,9532
Non-polymers241
Water1086
1
A: Small ubiquitin-related modifier,RNA-directed DNA polymerase
B: DNA
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)569,86318
Polymers569,71812
Non-polymers1466
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.5, -0.866025404), (0.866025404, -0.5), (1)314.208185, 84.1918295
3generate(-0.5, 0.866025404), (-0.866025404, -0.5), (1)84.1918295, 314.208185
4generate(-1), (1), (-1)265.60001, 265.60001
5generate(0.5, -0.866025404), (-0.866025404, -0.5), (-1)181.40818, 314.208185, 265.60001
6generate(0.5, 0.866025404), (0.866025404, -0.5), (-1)-48.6081755, 84.1918296, 265.60001

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Components

#1: Protein Small ubiquitin-related modifier,RNA-directed DNA polymerase / SUMO / Suppressor of mif two / Ubiquitin-like protein SMT3


Mass: 90781.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SUMO tag,SUMO tag
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Escherichia coli (E. coli)
Gene: SMT3, YDR510W, D9719.15, FV293_09650 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q12306
#2: DNA chain DNA


Mass: 4171.763 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the hexameric EcoDRT3b complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta 2 (DE3)
Buffer solutionpH: 7.5
Details: 20 mM HEPES-NaOH, 300 mM NaCl, 5 mM MgCl2, and 1 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9Servalcatmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13084 / Symmetry type: POINT
RefinementResolution: 3.1→3.1 Å / Num. reflection obs: 1609225 / Average fsc work: 0.8241
Displacement parametersBiso mean: 105.6 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.006557310.0118
ELECTRON MICROSCOPYs_angle_nonh_deg1.118577711.8374
ELECTRON MICROSCOPYs_dihedral_angle_1_deg4.52366382.5666
ELECTRON MICROSCOPYs_dihedral_angle_2_deg8.61851355.4074
ELECTRON MICROSCOPYs_dihedral_angle_3_deg12.8536147910
ELECTRON MICROSCOPYs_dihedral_angle_6_deg12.04427910
ELECTRON MICROSCOPYs_chiral_restr0.06148560.1315
ELECTRON MICROSCOPYs_planes0.006675980.02
ELECTRON MICROSCOPYs_nbd0.200686330.2
ELECTRON MICROSCOPYs_nbtor0.213984820.2
ELECTRON MICROSCOPYs_hbond_nbd0.15151620.2
ELECTRON MICROSCOPYs_symmetry_nbd0.18791080.2
ELECTRON MICROSCOPYs_symmetry_hbond_nbd0.217680.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.9-2.934ELECTRON MICROSCOPY561570.5194
2.935-2.967ELECTRON MICROSCOPY512950.5545
2.968-3.001ELECTRON MICROSCOPY498450.5826
3.001-3.035ELECTRON MICROSCOPY486370.6124
3.035-3.07ELECTRON MICROSCOPY472390.6435
3.071-3.106ELECTRON MICROSCOPY465690.6723
3.106-3.143ELECTRON MICROSCOPY457690.6936
3.143-3.181ELECTRON MICROSCOPY440670.7027
3.181-3.219ELECTRON MICROSCOPY432730.7221
3.219-3.259ELECTRON MICROSCOPY423330.7414
3.259-3.299ELECTRON MICROSCOPY415930.7619
3.299-3.341ELECTRON MICROSCOPY400150.7964
3.341-3.383ELECTRON MICROSCOPY391890.8226
3.384-3.427ELECTRON MICROSCOPY378610.8433
3.427-3.472ELECTRON MICROSCOPY374550.8641
3.472-3.518ELECTRON MICROSCOPY363730.8727
3.518-3.565ELECTRON MICROSCOPY350130.8816
3.565-3.613ELECTRON MICROSCOPY348490.8912
3.614-3.663ELECTRON MICROSCOPY333430.9039
3.664-3.714ELECTRON MICROSCOPY328650.9177
3.715-3.767ELECTRON MICROSCOPY312850.9253
3.767-3.821ELECTRON MICROSCOPY306030.9299
3.822-3.877ELECTRON MICROSCOPY303130.9352
3.877-3.934ELECTRON MICROSCOPY287410.9401
3.935-3.993ELECTRON MICROSCOPY284550.9457
3.994-4.055ELECTRON MICROSCOPY271570.9468
4.055-4.117ELECTRON MICROSCOPY270450.9436
4.118-4.182ELECTRON MICROSCOPY257770.9434
4.184-4.249ELECTRON MICROSCOPY244350.9465
4.25-4.318ELECTRON MICROSCOPY242770.9469
4.319-4.39ELECTRON MICROSCOPY233170.9499
4.39-4.463ELECTRON MICROSCOPY228510.9534
4.464-4.539ELECTRON MICROSCOPY217450.9511
4.54-4.619ELECTRON MICROSCOPY210330.9494
4.619-4.7ELECTRON MICROSCOPY207130.9503
4.701-4.785ELECTRON MICROSCOPY196470.95
4.786-4.873ELECTRON MICROSCOPY188410.9448
4.874-4.963ELECTRON MICROSCOPY182170.944
4.965-5.058ELECTRON MICROSCOPY177270.9478
5.059-5.157ELECTRON MICROSCOPY171250.9489
5.158-5.258ELECTRON MICROSCOPY161250.9422
5.26-5.365ELECTRON MICROSCOPY158710.9289
5.366-5.475ELECTRON MICROSCOPY152250.9208
5.477-5.591ELECTRON MICROSCOPY145330.9166
5.592-5.711ELECTRON MICROSCOPY137530.9153
5.712-5.835ELECTRON MICROSCOPY130590.9059
5.838-5.967ELECTRON MICROSCOPY129730.8892
5.97-6.105ELECTRON MICROSCOPY120210.8777
6.106-6.246ELECTRON MICROSCOPY117310.8741
6.25-6.399ELECTRON MICROSCOPY109810.8842
6.4-6.557ELECTRON MICROSCOPY107250.8916
6.559-6.722ELECTRON MICROSCOPY101170.8803
6.725-6.897ELECTRON MICROSCOPY93750.8619
6.899-7.078ELECTRON MICROSCOPY91330.8592
7.083-7.275ELECTRON MICROSCOPY85770.869
7.277-7.479ELECTRON MICROSCOPY82270.8599
7.482-7.693ELECTRON MICROSCOPY75970.8493
7.699-7.926ELECTRON MICROSCOPY73770.8542
7.929-8.169ELECTRON MICROSCOPY69010.863
8.173-8.429ELECTRON MICROSCOPY63030.8691
8.433-8.705ELECTRON MICROSCOPY60730.8778
8.709-8.994ELECTRON MICROSCOPY56130.8807
9.005-9.315ELECTRON MICROSCOPY52750.8765
9.321-9.653ELECTRON MICROSCOPY49810.8927
9.66-10.01ELECTRON MICROSCOPY45330.9044
10.024-10.41ELECTRON MICROSCOPY43030.9047
10.418-10.834ELECTRON MICROSCOPY40170.9087
10.843-11.294ELECTRON MICROSCOPY35650.9187
11.305-11.796ELECTRON MICROSCOPY33010.9254
11.807-12.33ELECTRON MICROSCOPY29910.9214
12.357-12.945ELECTRON MICROSCOPY28570.9126
12.96-13.607ELECTRON MICROSCOPY25170.9061
13.643-14.32ELECTRON MICROSCOPY21790.9199
14.362-15.159ELECTRON MICROSCOPY20850.9428
15.183-16.075ELECTRON MICROSCOPY18610.9358
16.104-17.109ELECTRON MICROSCOPY16690.9337
17.216-18.285ELECTRON MICROSCOPY13110.9298
18.328-19.58ELECTRON MICROSCOPY12490.9305
19.688-21.197ELECTRON MICROSCOPY10890.9385
21.334-23.03ELECTRON MICROSCOPY9070.9118
23.118-24.986ELECTRON MICROSCOPY7290.9185
25.324-27.842ELECTRON MICROSCOPY6250.9407
27.997-31.086ELECTRON MICROSCOPY5710.8601
31.301-35.18ELECTRON MICROSCOPY3810.9461
35.492-40.504ELECTRON MICROSCOPY3010.9852
40.983-46.952ELECTRON MICROSCOPY2250.9926
48.492-57.959ELECTRON MICROSCOPY1750.98
59.39-73.664ELECTRON MICROSCOPY1050.9954
76.672-93.904ELECTRON MICROSCOPY490.9915
108.431-265.6ELECTRON MICROSCOPY400.9465

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