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Yorodumi- EMDB-16793: Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16793 | |||||||||
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Title | Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S, C20S, C870S, T1279C mutant | |||||||||
Map data | Local resolution filtered map that was used for model building | |||||||||
Sample |
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Keywords | Bacterial toxin / Tc toxin / TOXIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Photorhabdus luminescens (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Nganga PN / Roderer D / Belyy A / Prumbaum D / Raunser S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: to be published Title: Kinetics of the syringe-like injection mechanism of Tc toxins Authors: Nganga PN / Folz J / Kucher S / Roderer D / Xu Y / Sitsel O / Belyy A / Prumbaum D / Assafa TE / Kuehnemuth R / Dong M / Seidel C / Bordignon E / Raunser S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16793.map.gz | 130.2 MB | EMDB map data format | |
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Header (meta data) | emd-16793-v30.xml emd-16793.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
Images | emd_16793.png | 108.9 KB | ||
Masks | emd_16793_msk_1.map emd_16793_msk_2.map | 216 MB 216 MB | Mask map | |
Filedesc metadata | emd-16793.cif.gz | 7.6 KB | ||
Others | emd_16793_additional_1.map.gz emd_16793_half_map_1.map.gz emd_16793_half_map_2.map.gz | 23.5 MB 171.8 MB 171.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16793 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16793 | HTTPS FTP |
-Validation report
Summary document | emd_16793_validation.pdf.gz | 914.2 KB | Display | EMDB validaton report |
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Full document | emd_16793_full_validation.pdf.gz | 913.8 KB | Display | |
Data in XML | emd_16793_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_16793_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16793 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16793 | HTTPS FTP |
-Related structure data
Related structure data | 8cq2MC 8cpzC 8cq0C 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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-Map
File | Download / File: emd_16793.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Local resolution filtered map that was used for model building | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16793_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_16793_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: A map that was used to model the...
File | emd_16793_additional_1.map | ||||||||||||
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Annotation | A map that was used to model the receptor binding region in the open state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half map
File | emd_16793_half_map_1.map | ||||||||||||
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Annotation | Second half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: First half map
File | emd_16793_half_map_2.map | ||||||||||||
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Annotation | First half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TcdA1
Entire | Name: TcdA1 |
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Components |
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-Supramolecule #1: TcdA1
Supramolecule | Name: TcdA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Molecular weight | Theoretical: 1.5 MDa |
-Macromolecule #1: TcdA1
Macromolecule | Name: TcdA1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Molecular weight | Theoretical: 285.329625 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAHHHHHHSS GLEVLFQGPM NESVKEIPDV LKSQSGFNSL TDISHSSFNE FRQQVSEHLS WSETHDLYHD AQQAQKDNRL YEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT R RPDLKSMA ...String: MAHHHHHHSS GLEVLFQGPM NESVKEIPDV LKSQSGFNSL TDISHSSFNE FRQQVSEHLS WSETHDLYHD AQQAQKDNRL YEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT R RPDLKSMA LSQQNMDIEL STLSLSNELL LESIKTESKL ENYTKVMEML STFRPSGATP YHDAYENVRE VIQLQDPGLE QL NASPAIA GLMHQASLLG INASISPELF NILTEEITEG NAEELYKKNF GNIEPASLAM PEYLKRYYNL SDEELSQFIG KAS NFGQQE YSNNQLITPV VNSSDGTVKV YRITREYTTN AYQMDVELFP FGGENYRLDY KFKNFYNASY LSIKLNDKRE LVRT EGAPQ VNIEYSANIT LNTADISQPF EIGLTRVLPS GSWAYAAAKF TVEEYNQYSF LLKLNKAIRL SRATELSPTI LEGIV RSVN LQLDINTDVL GKVFLTKYYM QRYAIHAETA LILCNAPISQ RSYDNQPSQF DRLFNTPLLN GQYFSTGDEE IDLNSG STG DWRKTILKRA FNIDDVSLFR LLKITDHDNK DGKIKNNLKN LSNLYIGKLL ADIHQLTIDE LDLLLIAVGE GKTNLSA IS DKQLATLIRK LNTITSWLHT QKWSVFQLFI MTSTSYNKTL TPEIKNLLDT VYHGLQGFDK DKADLLHVMA PYIAATLQ L SSENVAHSVL LWADKLQPGD GAMTAEKFWD WLNTKYTPGS SEAVETQEHI VQYCQALAQL EMVYHSTGIN ENAFRLFVT KPEMFGAATG AAPAHDALSL IMLTRFADWV NALGEKASSV LAAFEANSLT AEQLADAMNL DANLLLQASI QAQNHQHLPP VTPENAFSS WTSINTILQW VNVAQQLNVA PQGVSALVGL DYIQSMKETP TYAQWENAAG VLTAGLNSQQ ANTLHAFLDE S RSAALSTY YIRQVAKAAA AIKSRDDLYQ YLLIDNQVSA AIKTTRIAEA IASIQLYVNR ALENVEENAN SGVISRQFFI DW DKYNKRY STWAGVSQLV YYPENYIDPT MRIGQTKMMD ALLQSVSQSQ LNADTVEDAF MSYLTSFEQV ANLKVISAYH DNI NNDQGL TYFIGLSETD AGEYYWRSVD HSKFNDGKFA ANAWSEWHKI DCPINPYKST IRPVIYKSRL YLLWLEQKEI TKQT GNSKD GYQTETDYRY ELKLAHIRYD GTWNTPITFD VNKKISELKL EKNRAPGLYC AGYQGEDTLL VMFYNQQDTL DSYKN ASMQ GLYIFADMAS KDMCPEQSNV YRDNSYQQFD TNNVRRVNNR YAEDYEIPSS VSSRKDYGWG DYYLSMVYNG DIPTIN YKA ASSDLKIYIS PKLRIIHNGY EGQKRNQCNL MNKYGKLGDK FIVYTSLGVN PNNSSNKLMF YPVYQYSGNT SGLNQGR LL FHRDTTYPSK VEAWIPGAKR SLTNQNAAIG DDYATDSLNK PDDLKQYIFM TDSKGTATDV SGPVEINTAI SPAKVQII V KAGGKEQTFT ADKDVSIQPS PSFDEMNYQF NALEIDGSGL NFINNSASID VTFTAFAEDG RKLGYESFSI PVTLKVSTD NALTLHHNEN GAQYMQWQSY RTRLNTLFAR QLVARATTGI DTILSMETQN IQEPQLGKGF YATFVIPPYN LSTHGDERWF KLYIKHVVD NNSHIIYSGQ LTDTNINITL FIPLDDVPLN QDYHAKVYMT FKKSPSDGTW WGPHFVRDDK GIVTINPKSI L THFESVNV LNNISSEPMD FSGANSLYFW ELFYYTPMLV AQRLLHEQNF DEANRWLKYV WSPSGYIVHG QIQNYQWNVR PL LEDTSWN SDPLDSVDPD AVAQHDPMHY KVSTFMRTLD LLIARGDHAY RQLERDTLNE AKMWYMQALH LLGDKPYLPL STT WSDPRL DRAADITTQN AHDSAIVALR QNIPTPAPLS LRSANTLTDL FLPQINEVMM NYWQTLAQRV YNLRHNLSID GQPL YLPIY ATPADPKALL SAAVATSQGG GKLPESFMSL WRFPHMLENA RGMVSQLTQF GSTLQNIIER QDAEALNALL QNQAA ELIL TNLSIQDKTI EELDAEKTVL EKSKAGAQSR FDSYGKLYDE NINAGENQAM TLRASAAGLT TAVQASRLAG AAADLV PNI FGFAGGGSRW GAIAEATGYV MEFSANVMNT EADKISQSET YRRRRQEWEI QRNNAEAELK QIDAQLKSLA VRREAAV LQ KTSLKTQQEQ TQSQLAFLQR KFSNQALYNW LRGRLAAIYF QFYDLAVARC LMAEQAYRWE LNDDSARFIK PGAWQGTY A GLLAGETLML SLAQMEDAHL KRDKRALEVE RTVSLAEVYA GLPKDNGPFS LAQEIDKLVS QGSGSAGSGN NNLAFGAGT DTKTSLQASV SFADLKIRED YPASLGKIRR IKQISVTLPA LLGPYQDVQA ILSYGDKAGL ANGCEALAVS HGMNDSGQFQ LDFNDGKFL PFEGIAIDQG TLTLSFPNAS MPEKGKQATM LKTLNDIILH IRYTIK UniProtKB: TcdA1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 11.2 Component:
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Grid | Model: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 13059 / Average electron dose: 78.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8cq2: |