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- EMDB-51210: Bacteroides thetaiotaomicron siderophore transporter XusA in comp... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Bacteroides thetaiotaomicron siderophore transporter XusA in complex with surface-exposed lipoprotein XusB | |||||||||
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![]() | Outer membrane / membrane protein complex / siderophore transport / iron piracy / METAL TRANSPORT | |||||||||
Function / homology | ![]() siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Silale A / van den Berg B | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of iron piracy by human gut Bacteroides Authors: Silale A / Soo YL / Mark H / Basle A / van den Berg B | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 211 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.4 KB 23.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 97.9 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() ![]() | 398.2 MB 391.2 MB 391.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9gbcMC ![]() 9garC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Unsharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.74 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Sharpened map
File | emd_51210_additional_1.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
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-Half map: Half map 1
File | emd_51210_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_51210_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of TonB-dependent transporter XusA and surface-exposed li...
Entire | Name: Complex of TonB-dependent transporter XusA and surface-exposed lipoprotein XusB from Bacteroides thetaiotaomicron |
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Components |
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-Supramolecule #1: Complex of TonB-dependent transporter XusA and surface-exposed li...
Supramolecule | Name: Complex of TonB-dependent transporter XusA and surface-exposed lipoprotein XusB from Bacteroides thetaiotaomicron type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: XusB was tagged with an affinity tag on the chromosome. The tag was used to pull down the XusAB complex at native expression levels. |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: TonB-linked outer membrane receptor
Macromolecule | Name: TonB-linked outer membrane receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 89.255508 KDa |
Sequence | String: MINKSFLVFL AFLFSVSAFS QHGRSGGMIS GRVISTVEKE VVDFATVYLK GTNRGATTDE KGLYHLKAAA GDYTLVVSAI GYTTVEKKV TLKAGERIRV NVTIAPQVTE LNEVVVSTSA VSRVNKSAFN AVAIDAKGLH NSTQNLSDAL AKVPGLKLRE A GGVGSDMI ...String: MINKSFLVFL AFLFSVSAFS QHGRSGGMIS GRVISTVEKE VVDFATVYLK GTNRGATTDE KGLYHLKAAA GDYTLVVSAI GYTTVEKKV TLKAGERIRV NVTIAPQVTE LNEVVVSTSA VSRVNKSAFN AVAIDAKGLH NSTQNLSDAL AKVPGLKLRE A GGVGSDMI LSLDGFSGKH VKLFIDGVPQ EGVGSSFGLN NIPINFADRI EVYRGVVPVG FGTDALGGVI NIVTNKNRKN WF LDASYSY GSFNTHKSYV NFGQTFKNGL TYEINAFQNY SDNSYYVDTP VEEFYEGGGS AINTDKVEHV KRFHDNYHNE AVV GKVGLV DKKWADRLMI GLTYSRMYKE IQTGVVQKVV FGEKYRKGNS LMPSLEYRKR NLFVRNLDVA FTANYNRNFT NNVD TATYR FNWLGEKTSL KGRKGEQSYQ DMKSDNDNWN ATFTANYHIG TAHTFVLNHV LNTFHRENHN SVSVDESNAI AKVTR KNIT GFSYRLMPSE HWNLSVFGKY YNQYNAGPVS ASTSGTSNYV RLTNNVSSVG YGAAGTYFIL SGLQAKLSYE KAYRLP TNE ELFGDEDLEL GKIGLNPEKS DNLNFNLSYN RQLGKHGLYV ETGLIYRNTS DYIYRSIETT SNRSYGSYSN YGSVETK GY HISARYNYSC WVSIGGNFTQ MDVRDNVEKT QTGQESLTYG ARMPNLPYRF ANSDISFFWR NLWKKGNTLT VTYDNMYV H GFPLYSEALG AVETKDIVPT QFSHNLGITY SLKNGRYNVS FECKNFTDEK LYDNFSLQKA GRAFYGKVRV YFGGN UniProtKB: TonB-linked outer membrane receptor |
-Macromolecule #2: DUF4374 domain-containing protein
Macromolecule | Name: DUF4374 domain-containing protein / type: protein_or_peptide / ID: 2 Details: A C-terminal His6-tag coding sequence was fused to the xusB gene on the B. thetaiotaomicron chromosome. Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 51.686082 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKKNFLMWSF AMALLTGTLC TSCDETEGAV APEETQSVQK GIAITYLHVT DQIMKNRDVI RGENFLGNGE YVTFAGILEA NNKIYTAPI PMGLSVYGSA FEDGKWVKYP ELVKTEDGGS NSSSYEKGEL QWTQYPNEAW VAIYNDENFN NPTLIRTDKI S YACGRMRS ...String: MKKNFLMWSF AMALLTGTLC TSCDETEGAV APEETQSVQK GIAITYLHVT DQIMKNRDVI RGENFLGNGE YVTFAGILEA NNKIYTAPI PMGLSVYGSA FEDGKWVKYP ELVKTEDGGS NSSSYEKGEL QWTQYPNEAW VAIYNDENFN NPTLIRTDKI S YACGRMRS QYYQTIWAAD NGDVYVFSPS YAKIMDADVQ KTNLPAGVVR IKAGATDFDS YYCNLEELSG GKSFLRCWHI TG DYFLLQM YTGEINSRGT GATRMAVFKA TGNGDKGELY YVDGLPEPDR ISSFSGTPFC ENGVAYVGVI PITADGETNH PAI YKIDPV THTATKGLTV NATGITAIGR LAKDSHSTYV VSATVTSANS TANYLLATST LESGSVTPGN NNGFETATGT AWIF YKDQY LYRLQYNQGN EGVTTAYELN TNGGIAKRSN EYTITRFTTY GIFGENIISS SAVDATFTDH HHHHH UniProtKB: DUF4374 domain-containing protein |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 120 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 7 mg/mL | ||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 6645 / Average electron dose: 40.83 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: other / Details: ModelAngelo |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 57.2 |
Output model | ![]() PDB-9gbc: |