[English] 日本語
Yorodumi
- EMDB-0844: Signal substraction of TcdB1-TccC2 and part of TcdA1 -

+
Open data


ID or keywords:

Loading...

-
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
Keywordsprotein transportation / TcdA1 / TcdB1 / TccC2 / TOXIN-PROTEIN TRANSPORT complex
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 / : / TcdA1, receptor binding domain ...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 / : / TcdA1, receptor binding domain / : / TcdA1, receptor binding domain / 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 / : / Integrin alpha, N-terminal
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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

-
Structure visualization

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

emd_0844.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 380 pix.
= 508.44 Å		1.34 Å/pix.
x 380 pix.
= 508.44 Å		1.34 Å/pix.
x 380 pix.
= 508.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.338 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.06
Minimum - Maximum-1.1598004 - 0.69353884
Average (Standard dev.)0.00009251639 (±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

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

UniProtKB: TcdA1

-
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

UniProtKB: TcdB1

-
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

UniProtKB: TccC2

-
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

UniProtKB: TccC2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more