[English] 日本語
Yorodumi
- EMDB-50265: Active SV40 LTAg complex with DNA (3D variability component_002, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50265
TitleActive SV40 LTAg complex with DNA (3D variability component_002, frame_005).
Map dataVolume series map from continuous heterogeneity analysis postprocessed by EMReady. Frame_005 (of frames _000 thru _019) along principal component_002 (of components _000, 001, & _002).
Sample
  • Complex: SV40 large T antigen complex with DNA in presence of ATP and Mg2+.
    • Complex: Large T antigen
      • Protein or peptide: Large T antigen
    • Complex: DNA
      • DNA: Chains: S
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsAAA+ superfamily Helicase Substrate translocation DNA unwinding / DNA BINDING PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / : / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / isomerase activity / single-stranded DNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / : / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / isomerase activity / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / : / host cell nucleus / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus ...Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBetapolyomavirus macacae / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsShahid T
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_PC_17136 United Kingdom
Other private
CitationJournal: Nature / Year: 2025
Title: Structural dynamics of DNA unwinding by a replicative helicase.
Authors: Taha Shahid / Ammar U Danazumi / Muhammad Tehseen / Lubna Alhudhali / Alice R Clark / Christos G Savva / Samir M Hamdan / Alfredo De Biasio /
Abstract: Hexameric helicases are nucleotide-driven molecular machines that unwind DNA to initiate replication across all domains of life. Despite decades of intensive study, several critical aspects of their ...Hexameric helicases are nucleotide-driven molecular machines that unwind DNA to initiate replication across all domains of life. Despite decades of intensive study, several critical aspects of their function remain unresolved: the site and mechanism of DNA strand separation, the mechanics of unwinding propagation, and the dynamic relationship between nucleotide hydrolysis and DNA movement. Here, using cryo-electron microscopy (cryo-EM), we show that the simian virus 40 large tumour antigen (LTag) helicase assembles in the form of head-to-head hexamers at replication origins, melting DNA at two symmetrically positioned sites to establish bidirectional replication forks. Through continuous heterogeneity analysis, we characterize the conformational landscape of LTag on forked DNA under catalytic conditions, demonstrating coordinated motions that drive DNA translocation and unwinding. We show that the helicase pulls the tracking strand through DNA-binding loops lining the central channel, while directing the non-tracking strand out of the rear, in a cyclic process. ATP hydrolysis functions as an 'entropy switch', removing blocks to translocation rather than directly powering DNA movement. Our structures show the allosteric couplings between nucleotide turnover and subunit motions that enable DNA unwinding while maintaining dedicated exit paths for the separated strands. These findings provide a comprehensive model for replication fork establishment and progression that extends from viral to eukaryotic systems. More broadly, they introduce fundamental principles of the mechanism by which ATP-dependent enzymes achieve efficient mechanical work through entropy-driven allostery.
History
DepositionMay 10, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50265.png

Downloads & links

-
Map

FileDownload / File: emd_50265.map.gz / Format: CCP4 / Size: 36.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume series map from continuous heterogeneity analysis postprocessed by EMReady. Frame_005 (of frames _000 thru _019) along principal component_002 (of components _000, 001, & _002).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 213 pix.
= 213. Å		1 Å/pix.
x 213 pix.
= 213. Å		1 Å/pix.
x 213 pix.
= 213. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-0.10053748 - 15.569210999999999
Average (Standard dev.)0.086503424 (±0.82989514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions213213213
Spacing213213213
CellA=B=C: 213.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unpostprocessed volume series map from continuous heterogeneity analysis...

Fileemd_50265_additional_1.map
AnnotationUnpostprocessed volume series map from continuous heterogeneity analysis (5 A lowpass filter). Frame_005 (of frames _000 thru _019) along principal component_002 (of components _000, 001, & _002).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered and unmasked gold-standard half-map (consensus refinement)....

Fileemd_50265_half_map_1.map
AnnotationUnfiltered and unmasked gold-standard half-map (consensus refinement).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered and unmasked gold-standard half-map (consensus refinement)....

Fileemd_50265_half_map_2.map
AnnotationUnfiltered and unmasked gold-standard half-map (consensus refinement).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SV40 large T antigen complex with DNA in presence of ATP and Mg2+.

EntireName: SV40 large T antigen complex with DNA in presence of ATP and Mg2+.
Components
  • Complex: SV40 large T antigen complex with DNA in presence of ATP and Mg2+.
    • Complex: Large T antigen
      • Protein or peptide: Large T antigen
    • Complex: DNA
      • DNA: Chains: S
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: SV40 large T antigen complex with DNA in presence of ATP and Mg2+.

SupramoleculeName: SV40 large T antigen complex with DNA in presence of ATP and Mg2+.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: Large T antigen

SupramoleculeName: Large T antigen / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Betapolyomavirus macacae

-
Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: Large T antigen

MacromoleculeName: Large T antigen / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Betapolyomavirus macacae
Molecular weightTheoretical: 41.812664 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KQVSWKLVTE YAMETKCDDV LLLLGMYLEF QYSFEMCLKC IKKEQPSHYK YHEKHYANAA IFADSKNQKT ICQQAVDTVL AKKRVDSLQ LTREQMLTNR FNDLLDRMDI MFGSTGSADI EEWMAGVAWL HCLLPKMDSV VYDFLKCMVY NIPKKRYWLF K GPIDSGKT ...String:
KQVSWKLVTE YAMETKCDDV LLLLGMYLEF QYSFEMCLKC IKKEQPSHYK YHEKHYANAA IFADSKNQKT ICQQAVDTVL AKKRVDSLQ LTREQMLTNR FNDLLDRMDI MFGSTGSADI EEWMAGVAWL HCLLPKMDSV VYDFLKCMVY NIPKKRYWLF K GPIDSGKT TLAAALLELC GGKALNVNLP LDRLNFELGV AIDQFLVVFE DVKGTGGESR DLPSGQGINN LDNLRDYLDG SV KVNLEKK HLNKRTQIFP PGIVTMNEYS VPKTLQARFV KQIDFRPKDY LKHCLERSEF LLEKRIIQSG IALLLMLIWY RPV AEFAQS IQSRIVEWKE RLDKEFSLSV YQKMKFNVAM GIGVLD

UniProtKB: Large T antigen

-
Macromolecule #2: Chains: S

MacromoleculeName: Chains: S / type: dna / ID: 2
Details: Forked DNA. Annealed product of oligonucleotides TTCTGTGACTACCTGGACGACCGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT & TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCGGTCGTCCAGGTAGTCACAGA.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.388585 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
Details: 50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
GridModel: UltrAuFoil / Material: GOLD / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Details: 40 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8460 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
cryoSPARCNon-uniform refinement
cryoSPARC3DVA

Details: Consensus refinement. / Number images used: 201416
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: Non-uniform refinement
Final 3D classificationSoftware - Name: cryoSPARC

-
Atomic model buiding 1

Initial model
ChainDetails
source_name: Other, initial_model_type: experimental model"Static" LTAg-ATP-DNA model (to be separately deposited)
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9fa2:
Active SV40 LTAg complex with DNA (3D variability component_002, frame_005).

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more