+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39494 | |||||||||
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Title | Cryo-EM structure of ButCD complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | transporter / TonB-dependent / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides fragilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Xu JH / Chen Z / Gao X | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: A highly conserved SusCD transporter determines the import and species-specific antagonism of Bacteroides ubiquitin homologues Authors: Xu JH / Chen Z / Gao X | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39494.map.gz | 97.1 MB | EMDB map data format | |
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Header (meta data) | emd-39494-v30.xml emd-39494.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
Images | emd_39494.png | 83.5 KB | ||
Filedesc metadata | emd-39494.cif.gz | 5.7 KB | ||
Others | emd_39494_half_map_1.map.gz emd_39494_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39494 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39494 | HTTPS FTP |
-Validation report
Summary document | emd_39494_validation.pdf.gz | 798.1 KB | Display | EMDB validaton report |
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Full document | emd_39494_full_validation.pdf.gz | 797.7 KB | Display | |
Data in XML | emd_39494_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_39494_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39494 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39494 | HTTPS FTP |
-Related structure data
Related structure data | 8ypuMC 8yptC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_39494.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.18 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : ButCD complex
Entire | Name: ButCD complex |
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Components |
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-Supramolecule #1: ButCD complex
Supramolecule | Name: ButCD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacteroides fragilis (bacteria) |
-Macromolecule #1: Membrane protein
Macromolecule | Name: Membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacteroides fragilis (bacteria) |
Molecular weight | Theoretical: 48.007312 KDa |
Sequence | String: CDSYLDIRPV GSVIPQTAEE YRALLARAYL NVPNDRGLAC LRSDEMLVND NEYDRNSYGD IERWNDVSPF PGTSQFTWSN FYNVLFIAN QVIESQKEIT EGTPEVVNQL VGEAHLLRAY LHFVLVNLHG QPYTKSGALN SKSIPLKLDT DLEKTLGRNT V EEVYTSIL ...String: CDSYLDIRPV GSVIPQTAEE YRALLARAYL NVPNDRGLAC LRSDEMLVND NEYDRNSYGD IERWNDVSPF PGTSQFTWSN FYNVLFIAN QVIESQKEIT EGTPEVVNQL VGEAHLLRAY LHFVLVNLHG QPYTKSGALN SKSIPLKLDT DLEKTLGRNT V EEVYTSIL SDIEHARELI NKEKWETVFS YRFNVLSVDA LQSRVSLYMG AWPKCLESAE AVLAKKSVLV DMNETPLALP NH FESVESI TALEQVMGSS VNNAVWVPAT FLALYQEGDK RLAAYFAAPD ENGNRKSSKG GKREFSCTFR VGELYLNAAE AAA NMDKLP HARMRLLELM RKRYTPEAYA KKENAVNVMD KNALISEILN ERARELAFEG HRWFDLRRTT RPRMVKVLQG KTYI LEQDD PRYTIPIPRD AIAANPGL UniProtKB: Membrane protein |
-Macromolecule #2: SusC/RagA family TonB-linked outer membrane protein
Macromolecule | Name: SusC/RagA family TonB-linked outer membrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacteroides fragilis (bacteria) |
Molecular weight | Theoretical: 111.314523 KDa |
Sequence | String: DAVVVTGYQT VERRKLTAAV GKLNISDETI GAVKSIDQAL AGQIAGLSVT STSGAPGAPA KIRIRGTSSL NGTQDPLWVL DGIPLEGTD VPQSNVLNDV SNIQQSSIAG LNPADIENIT VLKDAAATAI YGARAANGVI VITTKKGKVG KPVINFSSKF T YMPTLSTN ...String: DAVVVTGYQT VERRKLTAAV GKLNISDETI GAVKSIDQAL AGQIAGLSVT STSGAPGAPA KIRIRGTSSL NGTQDPLWVL DGIPLEGTD VPQSNVLNDV SNIQQSSIAG LNPADIENIT VLKDAAATAI YGARAANGVI VITTKKGKVG KPVINFSSKF T YMPTLSTN RLNMLNSQEK VDLELELLRS NFAYGDNKGG VSKIISGYGL TDAYKKGGWS ALTPEAQTDI SRLRNTETDW GD ILFRDAF NQEYSLSLSG GNERVTYYTS IGYYQENGNV KGVGLDRLNI VAKTSYKVNR MLKFGVSLFV NRRNNKTYLT DTY GLVNPV YYSRKANPYY QPFDANGNYV YDFDVQNNSD TDLGFNIFEE RKNTSNEETI NALSSIFDAE LRFNDKLKFT TQLG LQLDK ASKEQIADKE SFSMRIIRKN SKYWDSASQS NKYFIPDGGV HKAYENTNSQ ITWKAMGEYR DSFNDIHELE VMVGT ELRK TWYETLFSAG YGFDRQTLTT KPVVFPDEDR ARQFPLHQKT YKENAYVSFF STASYSLMNR YTFGGSIRFD GSDLFG VDK KYRYLPLYSV SGLWRLSNEP FMQGTRKWMD NLAFRVSYGI QGNIDKNTSP FLLGKYIVDN ILPGGSEHMI DINSAPN KK LRWEKTQSVN VGLDFSVLNQ ALNLSVDYYY RKGTDLIGKQ MLPLETGFVS TNINWASMVN KGVEVSLSTR NVATKNFS W YTNLNFAYNN NKVLREAIPE AQTIPGREGY PVDAIFAIKT AGLDEEGYPL FYDKEGKKVT LKELYRLQDP FGLGFTVNS DVTPAEERSF YSYIGSQDTP YTGGLINTFS YKNWELTANL SFNLGGYVRT TPSYNFINFD RGQNVNSDIL DRWTPENTDG RLPALITSE KRADEYYWYD QKSEIYKNLD IWVKKLNYFR LQNLRLGYRL PEKMTKSLGM GSASVAIEGR NLLVFGSSYK N FLDPESMY NPYAPPIPKS ITFSLNLNF UniProtKB: SusC/RagA family TonB-linked outer membrane protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 619121 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |