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- EMDB-43754: BsaXI-DNA complex I -

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Basic information

Entry
Database: EMDB / ID: EMD-43754
TitleBsaXI-DNA complex I
Map dataBsaXI-DNA complex (P40-J522) conformation I map file P40-J538
Sample
  • Complex: Quaternary complex of RM, S and DNA complex
    • Protein or peptide: site-specific DNA-methyltransferase (adenine-specific)
    • Protein or peptide: S.BsaXI
    • DNA: DNA (41-MER) Top strand of BsaXI cognate DNA substrate
    • DNA: DNA (41-MER) Complementary strand of BsaXI DNA substrate
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: CALCIUM ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: water
Keywordsrestriction nuclease / restriction-modification systems / Type IIB / R-M complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


N-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding
Similarity search - Function
Type I restriction enzyme R protein, N-terminal domain / : / Type I restriction enzyme R protein N terminus (HSDR_N) / : / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. ...Type I restriction enzyme R protein, N-terminal domain / : / Type I restriction enzyme R protein N terminus (HSDR_N) / : / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Uncharacterized protein / Site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsShen BW / Stoddard BL / Xu S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Ro1-GM105691 United States
CitationJournal: To Be Published
Title: Structural and biochemical analysis of subunit assembly, DNA recognition and cleavage by a Type IIB restriction-modification enzyme: BsaXI
Authors: Shen BW / Heiter D / Xu S / Stoddard BL
History
DepositionFeb 20, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43754.png

Downloads & links

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Map

FileDownload / File: emd_43754.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBsaXI-DNA complex (P40-J522) conformation I map file P40-J538
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 330 pix.
= 369.6 Å		1.12 Å/pix.
x 330 pix.
= 369.6 Å		1.12 Å/pix.
x 330 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.33200872 - 0.80769074
Average (Standard dev.)0.00047588695 (±0.021524405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43754_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BsaXI-DNA J522 half map P40-J538-A

Fileemd_43754_half_map_1.map
AnnotationBsaXI-DNA J522 half map P40-J538-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BsaXI-DNA complex conformation I (J538) P40-J538-half-map-B

Fileemd_43754_half_map_2.map
AnnotationBsaXI-DNA complex conformation I (J538) P40-J538-half-map-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Quaternary complex of RM, S and DNA complex

EntireName: Quaternary complex of RM, S and DNA complex
Components
  • Complex: Quaternary complex of RM, S and DNA complex
    • Protein or peptide: site-specific DNA-methyltransferase (adenine-specific)
    • Protein or peptide: S.BsaXI
    • DNA: DNA (41-MER) Top strand of BsaXI cognate DNA substrate
    • DNA: DNA (41-MER) Complementary strand of BsaXI DNA substrate
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: CALCIUM ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: water

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Supramolecule #1: Quaternary complex of RM, S and DNA complex

SupramoleculeName: Quaternary complex of RM, S and DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Geobacillus stearothermophilus (bacteria) / Strain: Cpw230
Molecular weightTheoretical: 2.69 kDa/nm

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Macromolecule #1: site-specific DNA-methyltransferase (adenine-specific)

MacromoleculeName: site-specific DNA-methyltransferase (adenine-specific)
type: protein_or_peptide / ID: 1 / 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: Site-specific DNA-methyltransferase (adenine-specific)

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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: DNA (41-MER) Top strand of BsaXI cognate DNA substrate

MacromoleculeName: DNA (41-MER) Top strand of BsaXI cognate DNA substrate
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 16.083387 KDa
SequenceString: (DA)(DA)(DT)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA)(DT)(DT)(DG)(DT)(DC)(DG)(DG) (DA)(DA)(DC)(DC)(DA)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG)(DA) (DA) (DT)(DT)(DA)(DA)(DT)(DA) ...String:
(DA)(DA)(DT)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA)(DT)(DT)(DG)(DT)(DC)(DG)(DG) (DA)(DA)(DC)(DC)(DA)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG)(DA) (DA) (DT)(DT)(DA)(DA)(DT)(DA)(DA)(DG) (DC)(DT)(DA)(DG)

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Macromolecule #4: DNA (41-MER) Complementary strand of BsaXI DNA substrate

MacromoleculeName: DNA (41-MER) Complementary strand of BsaXI DNA substrate
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 15.963281 KDa
SequenceString: (DC)(DT)(DA)(DG)(DC)(DT)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DC)(DC)(DA)(DT)(DA)(DT) (DG)(DG)(6MA)(DG)(DA)(DC)(DT)(DT)(DG) (DG)(DT)(DT)(DC)(DC)(DG)(DA)(DC)(DA)(DA) (DT)(DA)(DT)(DT)(DC)(DA)(DG) ...String:
(DC)(DT)(DA)(DG)(DC)(DT)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DC)(DC)(DA)(DT)(DA)(DT) (DG)(DG)(6MA)(DG)(DA)(DC)(DT)(DT)(DG) (DG)(DT)(DT)(DC)(DC)(DG)(DA)(DC)(DA)(DA) (DT)(DA)(DT)(DT)(DC)(DA)(DG)(DC)(DT) (DT)(DA)(DT)(DT)

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Macromolecule #5: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.3 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Name: TrisHCl / Details: 20 mM TrisHCl, 250 mM Nacl, 2 mM CaCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was monodisperse.

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TALOS ARCTICA
TemperatureMin: 170.0 K
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingImage recording ID: 1 / Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-50 / Number grids imaged: 3 / Number real images: 1579 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.2 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureMin: 170.0 K / Max: 170.0 K
Specialist opticsPhase plate: OTHER
Image recordingImage recording ID: 2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: COUNTING / Digitization - Frames/image: 2-50 / Number grids imaged: 1 / Number real images: 2238 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 3000 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 245111
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: manual built model in coot
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-8w2p:
BsaXI-DNA complex I

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