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- EMDB-0844: Signal substraction of TcdB1-TccC2 and part of TcdA1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0844
TitleSignal substraction of TcdB1-TccC2 and part of TcdA1
Map dataB1C1 and part of A1
Sample
  • Complex: Toxin complex TcdA1-TcdB1-TccC2
    • Protein or peptide: TcdA1
    • Protein or peptide: TcdB1
    • Protein or peptide: TccC2
    • Protein or peptide: TccC2
Function / homology
Function and homology information


: / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / ABC toxin, N-terminal domain / ABC toxin N-terminal region ...Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / ABC toxin, N-terminal domain / ABC toxin N-terminal region / TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain / Rhs repeat-associated core
Similarity search - Domain/homology
TccC2 / TcdB1 / TcdA1
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYan ZF / Yang GW
CitationJournal: To Be Published
Title: Signal substraction of TcdB1-TccC2 and part of TcdA1
Authors: Yan ZF / Zhang N / Yang GW
History
DepositionNov 1, 2019-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l7i
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0844.png

Downloads & links

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Map

FileDownload / File: emd_0844.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB1C1 and part of A1
Voxel sizeX=Y=Z: 1.338 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.06
Minimum - Maximum-1.1598004 - 0.69353884
Average (Standard dev.)9.251639e-05 (±0.0062564625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 508.44003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3381.3381.338
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z508.440508.440508.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-1.1600.6940.000

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Supplemental data

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Sample components

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Entire : Toxin complex TcdA1-TcdB1-TccC2

EntireName: Toxin complex TcdA1-TcdB1-TccC2
Components
  • Complex: Toxin complex TcdA1-TcdB1-TccC2
    • Protein or peptide: TcdA1
    • Protein or peptide: TcdB1
    • Protein or peptide: TccC2
    • Protein or peptide: TccC2

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Supramolecule #1: Toxin complex TcdA1-TcdB1-TccC2

SupramoleculeName: Toxin complex TcdA1-TcdB1-TccC2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: TcdA1

MacromoleculeName: TcdA1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 20.255887 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RALEVERTVS LAEVYAGLPK DNGPFSLAQE IDKLVSQGSG SAGSGNNNLA FGAGTDTKTS LQASVSFADL KIREDYPASL GKIRRIKQI SVTLPALLGP YQDVQAILSY GDKAGLANGC EALAVSHGMN DSGQFQLDFN DGKFLPFEGI AIDQGTLTLS F PNASMPEK GKQATMLKTL NDIILHIRYT IK

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Macromolecule #2: TcdB1

MacromoleculeName: TcdB1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 165.296453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: TccC2

MacromoleculeName: TccC2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 74.759125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #4: TccC2

MacromoleculeName: TccC2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 1.905087 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
APEKGKYTKE VNFFDE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124828

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