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- EMDB-53035: Neobacillus vireti Wadjet-II JetABC dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-53035
TitleNeobacillus vireti Wadjet-II JetABC dimer
Map data
Sample
  • Complex: N. vireti JetABC dimer-of-tetramers
    • Protein or peptide: JetC
    • Protein or peptide: JetB
    • Protein or peptide: JetA
KeywordsSMC complexes / Wadjet / JetABCD / DNA loop extrusion / DNA BINDING PROTEIN
Biological speciesNeobacillus vireti LMG 21834 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.71 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: To Be Published
Title: Structure of a type II SMC Wadjet complex from Neobacillus vireti
Authors: Roisne-Hamelin F / Liu HW / Gruber S
History
DepositionMar 7, 2025-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53035.png

Downloads & links

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Map

FileDownload / File: emd_53035.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 400 pix.
= 580. Å		1.45 Å/pix.
x 400 pix.
= 580. Å		1.45 Å/pix.
x 400 pix.
= 580. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.27823418 - 0.67602855
Average (Standard dev.)0.00038481163 (±0.01686646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 580.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53035_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Full EM map.

Fileemd_53035_additional_1.map
AnnotationFull EM map.
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_53035_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_53035_half_map_2.map
Projections & Slices
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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
    • Protein or peptide: JetB
    • Protein or peptide: JetA

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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.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Neobacillus vireti LMG 21834 (bacteria)
Molecular weightTheoretical: 161.659016 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MMTEAKWVMN RAGLLNFWYY DDEIFPFSDG KLLLRGTNGS GKSVTMQSFL PVLLDGKKSP DRLDPFGSKA RRMEDYLLGE KEVVDRDER TGYLFIEYKK AGVERYITTG IGMQAKRHKG IKSWYFVITD NRRIGYDFEL AHSQLGDRVP FSAKELENRI G EGGYVVHT ...String:
MMTEAKWVMN RAGLLNFWYY DDEIFPFSDG KLLLRGTNGS GKSVTMQSFL PVLLDGKKSP DRLDPFGSKA RRMEDYLLGE KEVVDRDER TGYLFIEYKK AGVERYITTG IGMQAKRHKG IKSWYFVITD NRRIGYDFEL AHSQLGDRVP FSAKELENRI G EGGYVVHT QREYMELVNK YIFGFQSNEA YEDLIKLLIQ LRSPKLSKDF KPTVIYEILE SALPPLTDDE LRHLSDTIES MD QTQQQLE QLEREFASSS RLVNQYHSYN QYILAERAGK WQDALKRYTV AEEHVKGLTA QDEELTQEIK QEEEQKQQFA QQQ EIALEE KKRLERHEVW NLEEDKRKKI ENTKSLSSEI NSLQKKWDHK NSQYNRLWQE REQSQNQIRQ HESGMEDLLG ELQF DAEEA AFSEHEVNVH DFERHQEEEF DFSIWIGEIG SHEQLLANLN QLADEENRLS EEHNRLQRQS SEKKKEVDAI RKNLD HLAD WFTEEKQRLE HQVFTWIEQH PKLIFSNERR QEIARSIEGL YEENRYEQVR EKLLAVVNDY ITDISTKKKL METKIE DKK HELEAARAEL HHWKTLKMPN PDRAKDTEAF RLQLLEDGQA FIPFYAAVEF QDDVTEEQKE RIESALKQTG ILDSLIT EN ALAPTHDRVI RPEPQLLGYT LADYLRPDLE ADSLISNKLV DEILRSISLE QEGAGFHVDV DGSYSLGCLV GHAPNEGP S KYIGRSSRKR YQQEKIKECQ ETIEQLQLEL EELKVQLSQY EENLLQAAQW KQTMPTDQEL NDLNVQIEKT GHQLEEQKK VLFQLDEQWK QVHGHLQVIK IQLHQEGRQL NLSLTKEVLG QALISAKNYR DQLYSFKDLF QKCLFARKRI EDLTHRLFEM ETELDDLKG DQNVKESQLR KEKAEIESIE QQLKLKGIEE VRLRIQQVQQ ELREATEGIN HLLETIPQKK AKQETCQNEL A AAKTSAEF WSNMADEWEQ MVRADIARGF VEVVEMDPVK IVKQLESILG KYDRSKLNEQ LTKTFINEQI FLTEYRMFEY PE ETERPEW FSKEWGEYYE PFMNEWNQLQ SRRLILMEYK GQRVSPYFVF TSLEKELEDQ KGWLDEQDRQ LYEDIIVNTV GVI LRNRIK RAEKWVSEMD KIMESRDNSS GLTFSIAWKP LTAESEQELD TKDLVKLLQR NSKFLNEDDL NRITKHFQSR IGKA KELIQ LRNEGSTLHQ VLKEVLDYRK WFTFVLSFKR VNEPKRELTN NAFFKFSGGE KAMAMYIPLF TAAYSRYKEA GEMAP YIIS LDEAFAGVDE NNIRDMFEVV EQLGFNYIMN SQALWGDYDT ISSLSICELV RPKNADFVTV IRYQWDGKQR TFVVDD EHV EELVTHDG

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Macromolecule #2: JetB

MacromoleculeName: JetB / type: protein_or_peptide / ID: 2
Details: The last "G" in the theorical sequence is the result of a DNA cloning scar.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neobacillus vireti LMG 21834 (bacteria)
Molecular weightTheoretical: 46.569652 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MIMEQTQLFD EKAIQGMDIL FHHYWILRAE QPEWYQLIRE REKVLRRYLD EKFGLRLIVH QHFIKLEKIP VEPEGWMGIQ DFQEPMDYA IFCCALAFLE GKAVDEQFLL SELCQEIQAD YPGDFPLDWT LYTHRKSLIR AVKVLMEFQL IRTIDGDIGR F DQNEEQEV ...String:
MIMEQTQLFD EKAIQGMDIL FHHYWILRAE QPEWYQLIRE REKVLRRYLD EKFGLRLIVH QHFIKLEKIP VEPEGWMGIQ DFQEPMDYA IFCCALAFLE GKAVDEQFLL SELCQEIQAD YPGDFPLDWT LYTHRKSLIR AVKVLMEFQL IRTIDGDIGR F DQNEEQEV LYEASTYSRY FMRTYPDDFS SYQHWSELLK EDWKLNQEDE RRKRVYRKLF FSPGLHRLDQ QDPDFLYIRN YR NRLAEDI EKHSEYKLHV YKNTAFLSIA EPRQYQQVFP NSKASTDIIL QLSKYIHGEP ERFKANENGE ILMTEGEFEQ VVD DLRQQF GTGWAKYFRD MSTKGIRTEL LRAMKDWMMA EVDSETSLIR IKSLTGVMTG EYPSDFQTGG TEG

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Macromolecule #3: JetA

MacromoleculeName: JetA / type: protein_or_peptide / ID: 3
Details: "GPAA" at the begining of the theorical sequence is the remaining of the purification tag after tag cleavage. The last "G" in the theorical sequence is the result of a DNA cloning scar.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Neobacillus vireti LMG 21834 (bacteria)
Molecular weightTheoretical: 59.719617 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GPAAMDSTMK KIIEASYLTA DSAAHYRTIL RYFYHQHERM RDFIAPEELL EHMRSIPAFA DFQEDQLHQQ LAQLVKWNNL IARQDMTNA KTIEEYKKKR FRYQCTPYTV EIERMIVQLE KLGDTFQGSL ERSQFDRLFQ AITSLQNELE NDLNKSAEEY M RIWEDVFR ...String:
GPAAMDSTMK KIIEASYLTA DSAAHYRTIL RYFYHQHERM RDFIAPEELL EHMRSIPAFA DFQEDQLHQQ LAQLVKWNNL IARQDMTNA KTIEEYKKKR FRYQCTPYTV EIERMIVQLE KLGDTFQGSL ERSQFDRLFQ AITSLQNELE NDLNKSAEEY M RIWEDVFR YFQTIRTSTA DYIAYINSEQ TDQRMQTEAF LVYKNQFTTY LRDFIVSLQK TSLQIQHSLS ELTLERLQHF FQ KLIEHRG AIPRLEDVSS STNDWLTEYE EYWFSLRQWF LGSAVQQSEL DILQWQTNEM IRRMTRYVQR IGERQQHFRS RKK DYLQLS KWFVECRDSE EAHKLSAVVF GSMTIQHLQL EEATTENLHV DTWDEAPTEL TIKPRTVRYR EKTKPGSFNS NEQK KKEQR ELYLKEREQE KKLIEKYMTQ GKITLSALST VEPFIRKVLL SWIGKSMAAK NRMVKTDYGL HVKVMLDYEK TITLQ AEDG NLLMPDATFL FEETRG

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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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15908
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9qe0:
Neobacillus vireti Wadjet-II JetABC dimer

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