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- EMDB-53036: Neobacillus vireti Wadjet-II JetC hinge -

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Basic information

Entry
Database: EMDB / ID: EMD-53036
TitleNeobacillus vireti Wadjet-II JetC hinge
Map data
Sample
  • Complex: N. vireti JetABC dimer-of-tetramers
    • Protein or peptide: JetC
KeywordsSMC complexes / Wadjet / JetABCD / DNA loop extrusion / DNA BINDING PROTEIN
Biological speciesNeobacillus vireti LMG 21834 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.38 Å
AuthorsRoisne-Hamelin F / Gruber S
Funding supportEuropean Union, Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)724482European Union
Swiss National Science Foundation10001017 Switzerland
CitationJournal: Structure / Year: 2025
Title: Structure of a type II SMC Wadjet complex from Neobacillus vireti.
Authors: Florian Roisné-Hamelin / Hon Wing Liu / Stephan Gruber /
Abstract: Structural maintenance of chromosome complexes are essential DNA-folding motors that facilitate critical cellular functions, including chromosome segregation and DNA repair. Wadjet systems are ...Structural maintenance of chromosome complexes are essential DNA-folding motors that facilitate critical cellular functions, including chromosome segregation and DNA repair. Wadjet systems are prokaryotic SMC complexes specialized in cellular immunity against plasmids. Type I Wadjet systems restrict plasmids via a DNA extrusion-cleavage reaction. Two other Wadjet types (II and III) have also been identified, however, their molecular characteristics are unclear. Here, we reconstituted a representative type II Wadjet system from Neobacillus vireti. We show that this system shares substrate selection and cleavage properties with type I but exhibits distinctive structural features, including a long elbow-distal coiled coil, a channel-less hinge, and a tandem KITE subunit. These features help identify the common and distinguishing architectural elements in the family of Wadjet systems and raise intriguing questions about the evolution of prokaryotic SMC complexes.
History
DepositionMar 7, 2025-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53036.png

Downloads & links

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Map

FileDownload / File: emd_53036.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 300 pix.
= 435. Å		1.45 Å/pix.
x 300 pix.
= 435. Å		1.45 Å/pix.
x 300 pix.
= 435. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.3175837 - 0.80057
Average (Standard dev.)0.0011168895 (±0.016982911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 435.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53036_msk_1.map
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Additional map: Full EM map

Fileemd_53036_additional_1.map
AnnotationFull EM map
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Half map: #1

Fileemd_53036_half_map_1.map
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Half map: #2

Fileemd_53036_half_map_2.map
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Sample components

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Entire : N. vireti JetABC dimer-of-tetramers

EntireName: N. vireti JetABC dimer-of-tetramers
Components
  • Complex: N. vireti JetABC dimer-of-tetramers
    • Protein or peptide: JetC

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Supramolecule #1: N. vireti JetABC dimer-of-tetramers

SupramoleculeName: N. vireti JetABC dimer-of-tetramers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neobacillus vireti LMG 21834 (bacteria)

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Macromolecule #1: JetC

MacromoleculeName: JetC / type: protein_or_peptide / ID: 1
Details: The last "G" in the theorical sequence is the result of a DNA cloning scar.
Enantiomer: LEVO
Source (natural)Organism: Neobacillus vireti LMG 21834 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMTEAKWVMN RAGLLNFWYY DDEIFPFSDG KLLLRGTNGS GKSVTMQSFL PVLLDGKKSP DRLDPFGSKA RRMEDYLLGE KEVVDRDERT GYLFIEYKKA GVERYITTGI GMQAKRHKGI KSWYFVITDN RRIGYDFELA HSQLGDRVPF SAKELENRIG EGGYVVHTQR ...String:
MMTEAKWVMN RAGLLNFWYY DDEIFPFSDG KLLLRGTNGS GKSVTMQSFL PVLLDGKKSP DRLDPFGSKA RRMEDYLLGE KEVVDRDERT GYLFIEYKKA GVERYITTGI GMQAKRHKGI KSWYFVITDN RRIGYDFELA HSQLGDRVPF SAKELENRIG EGGYVVHTQR EYMELVNKYI FGFQSNEAYE DLIKLLIQLR SPKLSKDFKP TVIYEILESA LPPLTDDELR HLSDTIESMD QTQQQLEQLE REFASSSRLV NQYHSYNQYI LAERAGKWQD ALKRYTVAEE HVKGLTAQDE ELTQEIKQEE EQKQQFAQQQ EIALEEKKRL ERHEVWNLEE DKRKKIENTK SLSSEINSLQ KKWDHKNSQY NRLWQEREQS QNQIRQHESG MEDLLGELQF DAEEAAFSEH EVNVHDFERH QEEEFDFSIW IGEIGSHEQL LANLNQLADE ENRLSEEHNR LQRQSSEKKK EVDAIRKNLD HLADWFTEEK QRLEHQVFTW IEQHPKLIFS NERRQEIARS IEGLYEENRY EQVREKLLAV VNDYITDIST KKKLMETKIE DKKHELEAAR AELHHWKTLK MPNPDRAKDT EAFRLQLLED GQAFIPFYAA VEFQDDVTEE QKERIESALK QTGILDSLIT ENALAPTHDR VIRPEPQLLG YTLADYLRPD LEADSLISNK LVDEILRSIS LEQEGAGFHV DVDGSYSLGC LVGHAPNEGP SKYIGRSSRK RYQQEKIKEC QETIEQLQLE LEELKVQLSQ YEENLLQAAQ WKQTMPTDQE LNDLNVQIEK TGHQLEEQKK VLFQLDEQWK QVHGHLQVIK IQLHQEGRQL NLSLTKEVLG QALISAKNYR DQLYSFKDLF QKCLFARKRI EDLTHRLFEM ETELDDLKGD QNVKESQLRK EKAEIESIEQ QLKLKGIEEV RLRIQQVQQE LREATEGINH LLETIPQKKA KQETCQNELA AAKTSAEFWS NMADEWEQMV RADIARGFVE VVEMDPVKIV KQLESILGKY DRSKLNEQLT KTFINEQIFL TEYRMFEYPE ETERPEWFSK EWGEYYEPFM NEWNQLQSRR LILMEYKGQR VSPYFVFTSL EKELEDQKGW LDEQDRQLYE DIIVNTVGVI LRNRIKRAEK WVSEMDKIME SRDNSSGLTF SIAWKPLTAE SEQELDTKDL VKLLQRNSKF LNEDDLNRIT KHFQSRIGKA KELIQLRNEG STLHQVLKEV LDYRKWFTFV LSFKRVNEPK RELTNNAFFK FSGGEKAMAM YIPLFTAAYS RYKEAGEMAP YIISLDEAFA GVDENNIRDM FEVVEQLGFN YIMNSQALWG DYDTISSLSI CELVRPKNAD FVTVIRYQWD GKQRTFVVDD EHVEELVTHD G

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 22188 / 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: 2.6 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34013
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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