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- EMDB-43711: BsaXI -- Type IIB R-M system -

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Basic information

Entry
Database: EMDB / ID: EMD-43711
TitleBsaXI -- Type IIB R-M system
Map datacryosparc2_P35_J607, app BsaXI
Sample
  • Complex: heterotrimers of RM fusion and S subunit
    • Protein or peptide: RM.BsaXI
    • Protein or peptide: S.BsaXI
  • Ligand: S-ADENOSYLMETHIONINE
KeywordsR-M system / restriction nucleases / Type IIB / protein-DNA complex / BsaXI. / ANTIMICROBIAL PROTEIN
Function / homology: / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / DNA restriction-modification system / DNA binding / Uncharacterized protein / :
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsShen BW / Stoddard BL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105691 United States
CitationJournal: To Be Published
Title: Atomic insights into the mechanism of DNA recognition and methylation by type IIB restriction-modification system: CryoEM structures of DNA free and cognate DNA bound BsaXI.
Authors: Shen BW / Stoddard BL
History
DepositionFeb 13, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43711.png

Downloads & links

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Map

FileDownload / File: emd_43711.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryosparc2_P35_J607, app BsaXI
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.336 Å		1.08 Å/pix.
x 384 pix.
= 414.336 Å		1.08 Å/pix.
x 384 pix.
= 414.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.079 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.36282444 - 0.9502708
Average (Standard dev.)0.00029064124 (±0.017084736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: apoBsaXI; half map B CS P35 J607 B

Fileemd_43711_half_map_1.map
AnnotationapoBsaXI; half_map_B CS_P35_J607_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: apoBsaXI, half map A CS P35 607 A

Fileemd_43711_half_map_2.map
AnnotationapoBsaXI, half_map_A CS_P35_607_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : heterotrimers of RM fusion and S subunit

EntireName: heterotrimers of RM fusion and S subunit
Components
  • Complex: heterotrimers of RM fusion and S subunit
    • Protein or peptide: RM.BsaXI
    • Protein or peptide: S.BsaXI
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: heterotrimers of RM fusion and S subunit

SupramoleculeName: heterotrimers of RM fusion and S subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: reconstituted RM and S subunits of type IIB R-M systems.
Source (natural)Organism: Geobacillus stearothermophilus (bacteria) / Strain: Cpw230
Molecular weightTheoretical: 590 KDa

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Macromolecule #1: RM.BsaXI

MacromoleculeName: RM.BsaXI / type: protein_or_peptide / ID: 1 / Details: RM fusion protein / Number of copies: 2 / Enantiomer: LEVO
EC number: site-specific DNA-methyltransferase (adenine-specific)
Source (natural)Organism: Geobacillus stearothermophilus (bacteria) / Strain: Cpw230
Molecular weightTheoretical: 107.195234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKNWQRIVEA KLEQQKHKVA EISLENGTVN YSKKIKHNRN LKALTGDEEI VRAFLIDRLV NELDYKPEYL ETEKEYTIKG GHSKINPRV DVLVKDDKGN PFFFIEVKAP NKFEEDKDEI EGQLFALAQA EERDFKTKVK YLVYYTVELI DDEIVDRAII I DFEKYPTY ...String:
MKNWQRIVEA KLEQQKHKVA EISLENGTVN YSKKIKHNRN LKALTGDEEI VRAFLIDRLV NELDYKPEYL ETEKEYTIKG GHSKINPRV DVLVKDDKGN PFFFIEVKAP NKFEEDKDEI EGQLFALAQA EERDFKTKVK YLVYYTVELI DDEIVDRAII I DFEKYPTY TDWSNGGFIS TGTELTAGYG EPKKQPLIKG HEKYDLRVRI DREEIEGLGR NLHNVLWGGG GTNDSEIFYS LV NIILAKI QDEYEKEDGQ EYDFQVYQYG DNVESPQKLF DRINALYKRA LREQLNVTDE QKIAEDNVIN RNKFPLNKLV YTV QALESL SFLEGRNSLD GKDILGDFFE SIIRDGFKQT KGQFFTPTPI VKFILYALQL DKLAIDRLNN DRELPLIIDP SAGS GTFLI EAMKLITKEV KYKQNHKVKS SRQITKRFEE LFMPDHNENK WAREYLYGCE INFDLGTASK VNMILHGDGS ANIFV QDGL LPFRFYVKET SPNYLETASP DALYGDKEVN GKFDVVVSNP PFSVDLDTQT QREVRNAFLF GDKKNSENLF IERYYQ LLK EGGRLGVVLP ESVFDTTENK YIRLFIFKYF KVKAVVSLPQ VTFEPFTSTK TSLLFAQKKT KEEVEQWNEL WDKYGKE WS LLKTRINDYF SYFVKGRPLN KKWAPDVVKD IQEGNEDNIR KNIFRFLKDH IKEEDKNLEI KDLLIKYAEE ISSISKHE K ETDVFGFYNA WWVFGEVAKE LDYPIFMAEA ENVGYKRTKK GEKPMPNDLY DLEYAPSTLD CEKVLSSFDI EINALEASK TKLSVEKGLL EEKLKDKEDK ENEKIQKRLN KISELLETIE NQLDSIRSKK LEVEGILEKY YENNKLKEEY SERDDEELIN HFKHGVLYQ YRSEDILLRN KTVHKILDEI RQGVIWD

UniProtKB: UNIPROTKB: A0A4D7QEP1

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Macromolecule #2: S.BsaXI

MacromoleculeName: S.BsaXI / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria) / Strain: Cpw230
Molecular weightTheoretical: 55.038824 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGLIQRRNFS TFASEPSVRF DFNYMKSVTP TTEEYYTYKS LFEVVPSTVP TLDESEPFKY AEIGHVSKNG EVFPVTLSFE DRDELNEDL FKKIEKGDIF LPERGNILIS AIRPYLNKIV LIKEDDKTDI YFTKAFIQIK PLINSRILYY ALRTIFSEKI N AVSRQGKG ...String:
MGLIQRRNFS TFASEPSVRF DFNYMKSVTP TTEEYYTYKS LFEVVPSTVP TLDESEPFKY AEIGHVSKNG EVFPVTLSFE DRDELNEDL FKKIEKGDIF LPERGNILIS AIRPYLNKIV LIKEDDKTDI YFTKAFIQIK PLINSRILYY ALRTIFSEKI N AVSRQGKG YPTLKEDDLK TIQFSKKVID NLLAKEEELI SNIDALEKDI KELKSIQRSK KEIVDEVFSS HFNINMVELM AL DSQRRVD VGLSSISSLN STIRYSYRWN KMKLIQKYLY RDIDCIEPLG KYILSSNNGW SPESVVGGEG IPILGQEHLE FDG VLNVSP TKATTKTKNN MENFFIQEGD LFISRGNTVD LVGLACVVET EVTEDIIYPD LYIRLKIDEK VIHKKYLALL FNSF FGRLY FKYVSKGKNQ TMVKISSNEL LNYYLPIPPM EEQLEIVGKI EEQIGAQNEI EKQIEEKRNQ IRVIIEETAR S

UniProtKB: Uncharacterized protein

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Macromolecule #3: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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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

Concentration0.35 mg/mL
BufferpH: 8 / Details: 20 mM TrisHCl, ph 8.0, 2 mM CaCl2, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-50 / Number grids imaged: 1 / Number real images: 6227 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2487316
CTF correctionSoftware - Name: cryoSPARC (ver. 3.32) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: The alpha carbon trace of a phyr2 structure prediction for the methyl transferase domain was ducked into the refined map and was used as reference for manual building of the RM ...In silico model: The alpha carbon trace of a phyr2 structure prediction for the methyl transferase domain was ducked into the refined map and was used as reference for manual building of the RM model, including the alpha carbon of the Knocker and Paddle domains.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.32) / Number images used: 194038
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.32)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.32)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.32)
FSC plot (resolution estimation)

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