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Yorodumi- EMDB-16792: Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K567... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16792 | |||||||||
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Title | Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K567W K2008W mutant | |||||||||
Map data | The local 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: 3.2 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_16792.map.gz | 19.5 MB | EMDB map data format | |
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Header (meta data) | emd-16792-v30.xml emd-16792.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_16792.png | 123 KB | ||
Masks | emd_16792_msk_1.map | 669.9 MB | Mask map | |
Filedesc metadata | emd-16792.cif.gz | 7.4 KB | ||
Others | emd_16792_half_map_1.map.gz emd_16792_half_map_2.map.gz | 541.1 MB 540.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16792 | HTTPS FTP |
-Validation report
Summary document | emd_16792_validation.pdf.gz | 854.7 KB | Display | EMDB validaton report |
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Full document | emd_16792_full_validation.pdf.gz | 854.3 KB | Display | |
Data in XML | emd_16792_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_16792_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16792 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16792 | HTTPS FTP |
-Related structure data
Related structure data | 8cq0MC 8cpzC 8cq2C 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_16792.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The local filtered map that was used for model building | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_16792_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: First half map
File | emd_16792_half_map_1.map | ||||||||||||
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Annotation | First half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half map
File | emd_16792_half_map_2.map | ||||||||||||
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Annotation | Second 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: 285.489844 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAHHHHHHSS GLEVLFQGPM NESVKEIPDV LKSQCGFNCL TDISHSSFNE FRQQVSEHLS WSETHDLYHD AQQAQKDNRL YEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT R RPDLKSMA ...String: MAHHHHHHSS GLEVLFQGPM NESVKEIPDV LKSQCGFNCL 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 LLWITDHDNK 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 VTPENAFSC 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 KDMTPEQSNV 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 GWLPESFMSL 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 R2/1 / Material: COPPER / Mesh: 300 / 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: 2 / Number real images: 24611 / Average electron dose: 57.0 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: 1.5 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-8cq0: |