[English] 日本語
Yorodumi
- EMDB-45190: Yersinia entomophaga holotoxin complex in prepore conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45190
TitleYersinia entomophaga holotoxin complex in prepore conformation
Map data
Sample
  • Complex: Yersinia entomophaga holotoxin complex in pre-pore conformation
    • Protein or peptide: Toxin subunit YenA1
    • Protein or peptide: Toxin subunit YenA2
    • Protein or peptide: Chitinase 2
    • Protein or peptide: Toxin subunit YenB
    • Protein or peptide: Toxin subunit YenC2
KeywordsToxin / pore-forming / insecticidal / chitinases
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region / cytoplasm
Similarity search - Function
YwqJ-like deaminase / YwqJ-like deaminase / 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 ...YwqJ-like deaminase / YwqJ-like deaminase / 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 / 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 / Regulator of chromosome condensation (RCC1) signature 2. / Rhs repeat-associated core / : / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Integrin alpha, N-terminal / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Toxin subunit YenA1 / Toxin subunit YenA2 / Chitinase 2 / Toxin subunit YenB / Toxin subunit YenC2
Similarity search - Component
Biological speciesYersinia entomophaga (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLow YS / Landsberg MJ
Funding support Australia, 2 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220101681 Australia
Australian Research Council (ARC)DP170104484 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins.
Authors: Yu Shang Low / Solace G Roche / Nadezhda A Aleksandrova / Gabriel Foley / Jason Kk Low / Joseph K Box / Tristan I Croll / Irene R Chassagnon / J Shaun Lott / Evelyne Deplazes / Mikael Bodén ...Authors: Yu Shang Low / Solace G Roche / Nadezhda A Aleksandrova / Gabriel Foley / Jason Kk Low / Joseph K Box / Tristan I Croll / Irene R Chassagnon / J Shaun Lott / Evelyne Deplazes / Mikael Bodén / Mark Rh Hurst / Sarah J Piper / Michael J Landsberg /
Abstract: ABC toxins are toxin-translocating, pore-forming proteins found in a wide range of insecticidal bacteria and some mammalian pathogens. The Yersinia entomopahaga toxin complex (YenTc) belongs to a ...ABC toxins are toxin-translocating, pore-forming proteins found in a wide range of insecticidal bacteria and some mammalian pathogens. The Yersinia entomopahaga toxin complex (YenTc) belongs to a distinct subclass of ABC toxins, defined by a divergent molecular architecture. Structural details that define their mechanism of action remain to be elucidated. Here we determine structures of the YenTc holotoxin assembly in both prepore and pore-forming configurations using cryo-EM in conjunction with Alphafold2-assisted structural modelling of flexible domains. We define the structural mechanism via which enzymatically-active chitinase subunits are incorporated, and show using phylogenetic analyses that this subclass-defining feature has evolved relatively recently. Our structures point to the existence of distinct conformational states in YenTc, which may distinguish it from other structurally-characterised ABC toxins, or represent states on a shared mechanistic trajectory. Thus, our findings enhance our understanding of the structural diversity that defines distinct ABC toxin subclasses.
History
DepositionJun 4, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45190.png

Downloads & links

-
Map

FileDownload / File: emd_45190.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 468 pix.
= 804.96 Å		1.72 Å/pix.
x 468 pix.
= 804.96 Å		1.72 Å/pix.
x 468 pix.
= 804.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.345
Minimum - Maximum-0.58950025 - 1.4004049
Average (Standard dev.)-0.0002514608 (±0.05302145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions468468468
Spacing468468468
CellA=B=C: 804.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_45190_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_45190_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Yersinia entomophaga holotoxin complex in pre-pore conformation

EntireName: Yersinia entomophaga holotoxin complex in pre-pore conformation
Components
  • Complex: Yersinia entomophaga holotoxin complex in pre-pore conformation
    • Protein or peptide: Toxin subunit YenA1
    • Protein or peptide: Toxin subunit YenA2
    • Protein or peptide: Chitinase 2
    • Protein or peptide: Toxin subunit YenB
    • Protein or peptide: Toxin subunit YenC2

-
Supramolecule #1: Yersinia entomophaga holotoxin complex in pre-pore conformation

SupramoleculeName: Yersinia entomophaga holotoxin complex in pre-pore conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 2.5 MDa

-
Macromolecule #1: Toxin subunit YenA1

MacromoleculeName: Toxin subunit YenA1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 129.91232 KDa
SequenceString: MDKYNNYSNV IKNKSSISPL LAAAAKIEPE ITVLSSASKS NRSQYSQSLA DTLLGLGYRS IFDIAKVSRQ RFIKRHDESL LGNGAVIFD KAVSMANQVL QKYRKNRLEK SNSPLVPQTS SSTDASSESQ TNKLPEYNQL FPEPWDNFCR PGAIEALDSP A SYLLDLYK ...String:
MDKYNNYSNV IKNKSSISPL LAAAAKIEPE ITVLSSASKS NRSQYSQSLA DTLLGLGYRS IFDIAKVSRQ RFIKRHDESL LGNGAVIFD KAVSMANQVL QKYRKNRLEK SNSPLVPQTS SSTDASSESQ TNKLPEYNQL FPEPWDNFCR PGAIEALDSP A SYLLDLYK FIQSVELDGS NQARKLETRR ADIPKLSLDN DALYKEVTAL SIVNDVLSGS AREYIDQSGQ ADKAVNQILG DT HFPFTLP YSLPTQQINK GLGASNIELG TVIQRVDPQF SWNTTQEKYN QVLLAYTQLS SEQIALLSLP DVFTQNFLTQ TEL SAGYLS ASTTEILAEK DLSRHGYIVK AADNIKGPTQ LVEHSDASYD VIELTCTNQA KETITVKLRG ENIITYQRTK ARMV PFDNS SPFSRQLKLT FVAEDNPSLG NLDKGPYFAN MDIYAAEWVR ENVSSETMVS RPFLTMTYRI AIAKAGASLE ELQPE ADAF FINNFGLSAE DSSQLVKLVA FGDQTGSKAE EIESLLSCGE NLPIVSPNVI FANPIFGSYF NDEPFPAPYH FGGVYI NAH QRNAMTIIRA EGGREIQSLS NFRLERLNRF IRLQRWLDLP SHQLDLLLTS VMQADADNSQ QEITEPVLKS LGLFRHL NL QYKITPEIFS SWLYQLTPFA VSGEIAFFDR IFNREQLFDQ PFILDGGSFT YLDAKGSDAK SVKQLCAGLN ISAVTFQF I APLVQSALGL EAGTLVRSFE VVSSLYRLVS IPQTFGLSTE DGLILMNILT DEMGYLAKQP AFDDKQTQDK DFLSIILKM EALSAWLTKN NLTPASLALL LGVTRLAVVP TNNMVTFFKG IANGLSENVC LTTDDFQRQE LEGADWWTLL STNQVIDDMG LVLDIHPVW GKSDEEMLME KIQSIGVSND NNTLSIIVQI LIQAKNAQEN LLSQTISAEY GVERSVVPLQ LRWLGSNVYS V LNQVLNNT PTDISSIVPK LSELTYSLLI YTQLINSLKL NKEFIFLRLT QPNWLGLTQP KLSTQLSLPE IYLITCYQDW VV NANKNED SIHEYLEFAN IKKTEAEKTL VDNSEKCAEL LAEILAWDAG EILKAASLLG LNPPQATNVF EIDWIRRLQT LSE KTMIST EYLWQMGDLT ENSEFSLKEG VGEAVMAALK AQGDSDNV

UniProtKB: Toxin subunit YenA1

-
Macromolecule #2: Toxin subunit YenA2

MacromoleculeName: Toxin subunit YenA2 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 156.324938 KDa
SequenceString: MSNSIEAKLQ EDLRDALVDY YLGQIVPNSK DFTNLRSTIK NVDDLYDHLL LDTQVSAKVI TSRLSLVTQS VQQYINRIAL NLEPGLSIN QQEATDWEEF ANRYGYWAAN QQLRMFPEIY VDPTLRLTKT EFFFQLESAL NQGKLTDDVA QKAVLGYLNN F EEVSNLEI ...String:
MSNSIEAKLQ EDLRDALVDY YLGQIVPNSK DFTNLRSTIK NVDDLYDHLL LDTQVSAKVI TSRLSLVTQS VQQYINRIAL NLEPGLSIN QQEATDWEEF ANRYGYWAAN QQLRMFPEIY VDPTLRLTKT EFFFQLESAL NQGKLTDDVA QKAVLGYLNN F EEVSNLEI IAGYQDGIDI ENDKTYFVAR TRMQPYRYFW RSLDASQRNA NSQELYPTAW SEWKAISVPL ENVANGIVRP IM MDNRLYI SWFEVAEEKE TDSDGNIIVS GRYRTKIRLA HLGFDGVWSS GTTLREEVLA DQMEEMIAVV DRMEDEPRLA LVA FKEMSE SWDVVFSYIC DSMLIESSNL PTTTHPPKPG DGDKGLSDLD DYGANLVWFY LHETANGGKA EYKQLILYPV IINR DWPIE LDKTHQGDFG TVDDFTLNSN YTGDELSLYL QSSSTYKYDF SKSKNIIYGI WKEDANNNRC WLNYKLLTPE DYEPQ INAT LVMCDKGDVN IITGFSLPNG GVDAGGKIKV TLRVGKKLRD KFQIKQFSQT QYLQFPEASS ADVWYIGKQI RLNTLF AKE LIGKASRSLD LVLSWETQNS RLEEAILGGA AELIDLDGAN GIYFWELFFH MPFMVSWRFN VEQRYEDANR WVKYLFN PF ECEDEPALLL GKPPYWNSRP LVDEPFKGYS LTQPSDPDAI AASDPIHYRK AVFNFLTKNI IDQGDMEYRK LQPSARTL A RLSYSTASSL LGRRPDVQLT SFWQPLTLED ASYKTDSEIR AIEMQSQPLT FEPVVHDQTM SAVDNDIFMY PMNNELRGL WDRIENRIYN LRHNLTLDGK EINMDLYDSS ISPRGLMKQR YQRVVTARNA SKMNFKVPNY RFEPMLNRSK SGVETLIQFG STLLSLLER KDSLSFDAYQ MIQSGDLYRF SIDLQQQDID INKASLEALQ VSKQSAQDRY DHFKELYDEN ISSTEQKVIE L QSQAANSL LMAQGMRTAA AALDVIPNIY GLAVGGSHWG APLNAAAEII MIKYQADSSK SESLSVSESY RRRRQEWELQ YK QAEWEVN SVEQQINLQN MQIKAANKRL EQVEAQQQQA MALLDYFSER FTNESLYTWL ISQLSSLYLQ AYDAVLSLCL SAE ASLLYE LNLGEQSFVG GGGWNDLYQG LMAGETLKLA LMRMERVYVE QNSRRQEITK TISLKALLGE SWPAELNKLK QKTP INFNL EEQIFVEDYQ ELYQRRIKSV SVSLPMLVGP YEDVCAQLTQ TSSSYSTRAD LKTVENMLTK RTFADTPHLV RSIQP NQQI SLSTGVNDSG LFMLNFDDER FLPFEGSGVD SSWRLQFTNL KQNLDSLNDV ILHVKYTAAI GSSTFSQGVR KILANI NND E

UniProtKB: Toxin subunit YenA2

-
Macromolecule #3: Chitinase 2

MacromoleculeName: Chitinase 2 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO / EC number: chitinase
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 69.740609 KDa
SequenceString: MVNKYTYTSS KAMSDISDVI GEPLAAWDSQ VGGRVFNVIF DGKVYTNTYW VERWQVPGIG SSDGNPHNAW KFVRAATADE INKIGNPTT ADVKPTENIP SPILVEDKYT EETYSRPDVN FKEDGSQGNL SYTATRVCAP MYNHYVGDKT KPKLSAYITD W CQYDARLD ...String:
MVNKYTYTSS KAMSDISDVI GEPLAAWDSQ VGGRVFNVIF DGKVYTNTYW VERWQVPGIG SSDGNPHNAW KFVRAATADE INKIGNPTT ADVKPTENIP SPILVEDKYT EETYSRPDVN FKEDGSQGNL SYTATRVCAP MYNHYVGDKT KPKLSAYITD W CQYDARLD GGGSKEEERG RGFDLATLMQ NPATYDRLIF SFLGICGDIG NKSKKVQEVW DGWNAQAPSL GLPQIGKGHI VP LDPYGDL GTARNVGLPP ESADTSIESG TFLPYYQQNR AAGLLGGLRE LQKKAHAMGH KLDLAFSIGG WSLSSYFSAL AEN PDERRV FVASVVDFFV RFPMFSCVDI DWEYPGGGGD EGNISSDKDG ENYVLLIKEL RSALDSRFGY SNRKEISIAC SGVK AKLKK SNIDQLVANG LDNIYLMSYD FFGTIWADYI GHHTNLYSPK DPGEQELFDL SAEAAIDYLH NELGIPMEKI HLGYA NYGR SAVGGDLTTR QYTKNGPALG TMENGAPEFF DIVKNYMDAE HSLSMGKNGF VLMTDTNADA DFLFSEAKGH FISLDT PRT VKQKGEYAAK NKLGGVFSWS GDQDCGLLAN AAREGLGYVA DSNQETIDMG PLYNPGKEIY LKSISEIKSK

UniProtKB: Chitinase 2

-
Macromolecule #4: Toxin subunit YenB

MacromoleculeName: Toxin subunit YenB / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 167.147984 KDa
SequenceString: MQNSQEMAIT TLSLPKGGGA INGMGESVGQ AGPDGMVTFS IPLPFSAGRG VAPALSLSYS SGAGNGPFGM GWQCSAMSIS RRTQKGVPQ YNEDDEFLSP SGEVMAIALN DSGFEDVRTA NRLQGIPLPF SYKVTRYQPR LIQDFIKIEY WQPVKQTDGT P FWIIYSPD ...String:
MQNSQEMAIT TLSLPKGGGA INGMGESVGQ AGPDGMVTFS IPLPFSAGRG VAPALSLSYS SGAGNGPFGM GWQCSAMSIS RRTQKGVPQ YNEDDEFLSP SGEVMAIALN DSGFEDVRTA NRLQGIPLPF SYKVTRYQPR LIQDFIKIEY WQPVKQTDGT P FWIIYSPD GQTHILGKNS HSRVANAENP SQIASWLLEE TVTPTGEHIY YQYSGENQVN CTDAEIALHP QDSAQRYLAR ID YGNISPQ ASLFVLDEEL PNLTQWLFHL VFDYGERDIS INKIPTFEGG TTGWLARPDM FSRYDFGIEI RNRRLCHQVL GFH RLEALN DRDVTDEIPV LVNRLTLDYD LNNSVSTLVA VRQVAYETDG SPITQPPLEF DYQRFDTGSI PGWQEMPQLE AFNG YQPYQ MIDLYGEGTP GILYQETPGA WWYKSPQRQI GGDSNAVTYG AMKALPKIPR LQEGATLMDI NGDGRLDWVI TSAGV RGFH SIHSTGEWTH FTPLNTLPTE YFHPKAQLAD LVGAGLSDLV LIGPKSVRLY ANQQGNWAPA QDVTQAENVS LPVIGI DSR QLVAFADMLG SGQQHLVEIT ADSVKCWPNM GHGRFGQPLT LEGFSQPQTS FNPDRVFLAD IDGSGTNDII YAHSECL EI YLNESGNRFS KPISLLLPDG VNFDNTCQLQ AADIQGLGIA SLVMTVPHMS PTHWRCDLAL NKPWLLNVMN NNRGAETC L FYRSSAQFWL DEKQLVEAAG QQPECHLPFP MHLHWRSEIF DEITGNRLTQ EQEYAHGSWD GQEREFRGFG RLIQRDTDG FAQGTVDIPT HPSRTVSWFA TGIPEIDTTL SAEFWRGDDQ AFSPFSPRFT RWENDSEAGS DVAFIPSEHD AFWLNRAMKG QLLRSELYG DDGTPEAEIP YSVTEMRHQV RALPTTDATV PSAWCSTIET RSYQYQRVAA DPQCSQQVVI KADRYGSPLL S VAINYPRR KKPEKSPYPD DLPETLFDSS YDTQQQQLHL TKQQQNYFHL TNDDNWLLGL PKEQRNDGYQ YDQERAPANG FT LETLIAS NSLIGSNQPF TYLGQSRVAY QGGVDEQPSL QALVAYGETA ILDEKTLQAF VGVLDSKTRD ELLFSAGYQL APR LFRVES EPDVWVARQG YSEFGDYSQF WRPLSQRSTL LTGKTTLKWD KHYCVVIETQ DAAQLVTQAR YDYRFLTPYS LTDA NDNQH YVVLNPFGEV IASRFWGTEA GKDAGYSTPQ AKPFVVPATI EAALALSPGI PVAHCAIFEP ESWMQKLTQH DVSER MADN GTLWNALLQA RFVTEDGYVC ALGRRRWMAR HGLSVLMLTL LAEIPRTPPH SLTITTDRYD SDDQQQLRQR ILFSDG FGR LLQSAQRVEA GESWQRSEDS SLVVNVSGTP ALVVTDNRWA VSGRTEYDGK GQGIRVYQPY FLDDWRYLSD DSARTDL FA DTHIYDPLGR EYQVITAKGY RRERQYTPWF VVNQDENDTA ANLAI

UniProtKB: Toxin subunit YenB

-
Macromolecule #5: Toxin subunit YenC2

MacromoleculeName: Toxin subunit YenC2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 107.563875 KDa
SequenceString: MDIQLFSKTP SVTVFDNRGL SVRDIAYRRH PDTPKVTEEC ITYHQFDFRG FLAQSLDPRL NHKEVTNFSY LTDLNGNIIY TQSVDAGNT LVLNDTEGRS VIAMTNISRG ENGKDDLSLA VTRTFQYENA PLPGRPLSVT EQVNGENARI TEHFVYAGNT P QEKNLNLA ...String:
MDIQLFSKTP SVTVFDNRGL SVRDIAYRRH PDTPKVTEEC ITYHQFDFRG FLAQSLDPRL NHKEVTNFSY LTDLNGNIIY TQSVDAGNT LVLNDTEGRS VIAMTNISRG ENGKDDLSLA VTRTFQYENA PLPGRPLSVT EQVNGENARI TEHFVYAGNT P QEKNLNLA GQCVSYYDAA GLIQTDSVSL TGKPLSVSRK LLKNLDDTNI LADWQGNDTS AWNSLLATEI YTTVTRTDAA GA VLTTIDA VGNQQRVAFD IAGQLSASWL TLKGGQEQVI IKVLTYSAAG QKLREEGGNG VVTTYTYEAE TQRLIGIKTE RPN GHAAGA KVLQDLRYEY DPVGNVLSIT NDAEETRFWR NQKVVPENAY RYDSLYQLVS ASGREVAGAG QQGSDLPSPL VPLP SDSSV YTNYTRTYTY DSAGNLMRIR HSAPATNNNY TLNITVSERS NRGVMSSLTE NPADVDALFT ASGSQKCLQQ GQSLI WTPR GELRTVLLVA RGETADDSES YRYDGSSQRI LKISSQQTNH SARVQRALYL PGLEWRTMTG GVAEAENLQV ICIGEA GRA QVRVLHWESG KPDGIINDQI RWSYDNLTCS SGLEVDGDGL VISMEEYYPY GGTAVWAARS HIETAYKTVR YSGKERD AT GLYYYGFRYY QPWAGRWLSA DPAGTVDGLN LYRMVRNNPL RLTDPDGMAP LDWLDLDTTN ASRDIVKAIY QLNQIDGP H RGVRDTYQRM TESTGMILQE TLNNEAVLKG IKQKDKEKKS RGMKFTNSKL KTYAAHAGVL NTLQPDPVYK DGFLNLPGS LGNKNTFPGV ELIEDKVKPS LSQYHPDKLG KSQRWKPESS LGYYRVADTE AFITGIRSQY KSSGTDLHAV VEGRIRDHLL ANNNVLPKM AGIAGLHAEV QALNYIISNP DIEGGNAERL NGSYIFTQRL VGDVNQDFPA CYNCSGIISG LENVMTGRVN N DVRLKRRK SF

UniProtKB: Toxin subunit YenC2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI F30
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ogd

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60315
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelPDB ID:

6ogd


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot (ver. 0.8.9.3)
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9c4k:
Yersinia entomophaga holotoxin complex in prepore conformation

+
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