+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0844 | |||||||||
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Title | Signal substraction of TcdB1-TccC2 and part of TcdA1 | |||||||||
Map data | B1C1 and part of A1 | |||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Photorhabdus luminescens (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Yan ZF / Yang GW | |||||||||
Citation | Journal: To Be Published Title: Signal substraction of TcdB1-TccC2 and part of TcdA1 Authors: Yan ZF / Zhang N / Yang GW | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0844.map.gz | 12.8 MB | EMDB map data format | |
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Header (meta data) | emd-0844-v30.xml emd-0844.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_0844.png | 183.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0844 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0844 | HTTPS FTP |
-Validation report
Summary document | emd_0844_validation.pdf.gz | 299.3 KB | Display | EMDB validaton report |
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Full document | emd_0844_full_validation.pdf.gz | 298.8 KB | Display | |
Data in XML | emd_0844_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_0844_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0844 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0844 | HTTPS FTP |
-Related structure data
Related structure data | 6l7iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0844.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | B1C1 and part of A1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Toxin complex TcdA1-TcdB1-TccC2
Entire | Name: Toxin complex TcdA1-TcdB1-TccC2 |
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Components |
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-Supramolecule #1: Toxin complex TcdA1-TcdB1-TccC2
Supramolecule | Name: Toxin complex TcdA1-TcdB1-TccC2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-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: 20.255887 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RALEVERTVS LAEVYAGLPK DNGPFSLAQE IDKLVSQGSG SAGSGNNNLA FGAGTDTKTS LQASVSFADL KIREDYPASL GKIRRIKQI SVTLPALLGP YQDVQAILSY GDKAGLANGC EALAVSHGMN DSGQFQLDFN DGKFLPFEGI AIDQGTLTLS F PNASMPEK GKQATMLKTL NDIILHIRYT IK |
-Macromolecule #2: TcdB1
Macromolecule | Name: TcdB1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Molecular weight | Theoretical: 165.296453 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQNSQTFSVT ELSLPKGGGA ITGMGEALTP AGPDGMAALS LPLPISAGRG YAPSLTLNYN SGTGNSPFGL GWDCGVMAIR RRTSTGVPN YDETDTFLGP EGEVLVVALN EAGQADIRSE SSLQGINLGA TFTVTCYRSR LESHFNRLEY WQPQTTGATD F WLIYSPDG ...String: MQNSQTFSVT ELSLPKGGGA ITGMGEALTP AGPDGMAALS LPLPISAGRG YAPSLTLNYN SGTGNSPFGL GWDCGVMAIR RRTSTGVPN YDETDTFLGP EGEVLVVALN EAGQADIRSE SSLQGINLGA TFTVTCYRSR LESHFNRLEY WQPQTTGATD F WLIYSPDG QVHLLGKNPQ ARISNPLNVN QTAQWLLEAS ISSHSEQIYY QYRAEDEAGC ETDELAAHPS ATVQRYLQTV HY GNLTASD VFPTLNGDDP LKSGWMFCLV FDYGERKNSL SEMPLFKATG NWLCRKDRFS RYEYGFELRT RRLCRQILMF HRL QTLSGQ AKGDDEPALV SRLILDYDEN AMVSTLVSVR RVGHEDNNTV TALPPLELAY QPFEPEQTAL WQSMDVLANF NTIQ RWQLL DLKGEGVPGI LYQDRNGWWY RSAQRQAGEE MNAVTWGKMQ LLPITPAVQD NASLMDINGD GQLDWVITGP GLRGY HSQH PDGSWTRFTP LHALPIEYSH PRAQLADLMG AGLSDLVLIG PKSVRLYVNN RDGFTEGRDV VQSGDITLPL PGADAR KLV AFSDVLGSGQ AHLVEVSATQ VTCWPNLGHG RFGQPIVLPG FSQSAASFNP DRVHLADLDG SGPADLIYVH ADRLDIF SN ESGNGFAKPF TLSFPDGLRF DDTCQLQVAD VQGLGVVSLI LSVPHMAPHH WRCDLTNAKP WLLSETNNNM GANHTLHY R SSVQFWLDEK AAALATGQTP VCYLPFPVHT LWQTETEDEI SGNKLVTTLR YAHGAWDGRE REFRGFGYVE QTDSHQLAQ GNAPERTPPA LTKSWYATGL PAVDNALSAG YWRGDKQAFA GFTPRFTLWK EGKDVPLTPE DDHNLYWLNR ALKGQPLRSE LYGLDGSAQ QQIPYTVTES RPQVRQLQDG ATVSPVLWAS VVESRSYHYE RIISDPQCNQ DITLSSDLFG QPLKQVSVQY P RRNKPTTN PYPDTLPDTL FASSYDDQQQ LLRLTCRQSS WHHLIGNELR VLGLPDGTRS DAFTYDAKQV PVDGLNLETL CA ENSLIAD DKPREYLNQQ RTFYTDGKNQ TPLKTPTRQA LIAFTETAVL TESLLSAFDG GITPDELPGI LTQAGYQQEP YLF PRTGEN KVWVARQGYT DYGTEAQFWR PVAQRNSLLT GKMTLKWDTH YCVITQTQDA AGLTVSANYD WRFLTPTQLT DIND NVHLI TLDALGRPVT QRFWGIESGV ATGYSSSEEK PFSPPNDIDT AINLTGPLPV AQCLVYAPDS WMPLFSQETF NTLTQ EEQE TLRDSRIITE DWRICALTRR RWLQSQKIST PLVKLLTNSI GLPPHNLTLT TDRYDRDSEQ QIRQQVAFSD GFGRLL QAS VRHEAGEAWQ RNQDGSLVTK VENTKTRWAV TGRTEYDNKG QTIRTYQPYF LNDWRYVSDD SARKEAYADT HIYDPIG RE IRVITAKGWL RQSQYFPWFT VSEDENDTAA DALV |
-Macromolecule #3: TccC2
Macromolecule | Name: TccC2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Molecular weight | Theoretical: 74.759125 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSSYNSAIDQ KTPSIKVLDN RKLNVRTLEY LRTQADENSD ELITFYEFNI PGFQVKSTDP RKNKNQSGPN FIRVFNLAGQ VLREESVDA GRTITLNDIE SRPVLIINAT GVRQNHRYED NTLPGRLLAI TEQVQAGEKT TERLIWAGNT PQEKDYNLAG Q CVRHYDTA ...String: MSSYNSAIDQ KTPSIKVLDN RKLNVRTLEY LRTQADENSD ELITFYEFNI PGFQVKSTDP RKNKNQSGPN FIRVFNLAGQ VLREESVDA GRTITLNDIE SRPVLIINAT GVRQNHRYED NTLPGRLLAI TEQVQAGEKT TERLIWAGNT PQEKDYNLAG Q CVRHYDTA GLTQLNSLSL AGVVLSQSQQ LLVDDKNADW TGEDQSLWQQ KLSSDVYTTQ NKADATGALL TQTDAKGNIQ RL AYDVAGQ LKGCWLTLKG QAEQVIIKSL TYSAAGQKLR EEHGNGVITE YSYEPETQRL IGIATRRPSD AKVLQDLRYQ YDP VGNVIN IRNDAEATRF WRNQKVVPEN SYTYDSLYQL ISATGREMAN IGQQNNQLPS PALPSDNNTY TNYTRSYSYD HSGN LTQIR HSSPATQNNY TVAITLSNRS NRGVLSTLTT DPNQVDTLFD AGGHQTSLLP GQTLIWTPRG ELKQVNNGPG NEWYR YDSN GMRQLKVSEQ PTQNTTQQQR VIYLPGLELR TTQSNATTTE ELHVITLGEA GRAQVRVLHW ESGKPEDVNN NQLRYS YDN LIGSSQLELD NQGQIISEEE YYPFGGTALW AANSQTEASY KTIRYSGKER DATGLYYYGY RYYQPWAGRW LSADPAG TI DGLNLYRMVR NNPVSLQDEN GL |
-Macromolecule #4: TccC2
Macromolecule | Name: TccC2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Molecular weight | Theoretical: 1.905087 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: APEKGKYTKE VNFFDE |
-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/PHILIPS CM300FEG/HE |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124828 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |