[English] 日本語
Yorodumi
- EMDB-19984: Lymphostatin, conformation 2, N-terminal part -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19984
TitleLymphostatin, conformation 2, N-terminal part
Map datarelion map from Refine3D job, no sharpening
Sample
  • Complex: Lymphostatin
    • Protein or peptide: Lymphostatin
Keywordsbacterial virulence factor / glycosyltransferase / protease / TOXIN
Function / homology
Function and homology information


glycosyltransferase activity / cysteine-type endopeptidase activity
Similarity search - Function
Protein of unknown function DUF3491 / Protein of unknown function (DUF3491) / Peptidase C58, YopT-type domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGriessmann M / Rasmussen T / Bottcher B
Funding support Germany, 8 items
OrganizationGrant numberCountry
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)525040890 Germany
German Research Foundation (DFG)428774170 Germany
German Research Foundation (DFG)INST 93/903-1 Germany
German Research Foundation (DFG)INST 93/1042-1 Germany
German Research Foundation (DFG)93/1143-1 Germany
German Research Foundation (DFG)BO1150/18-1 Germany
CitationJournal: to be published
Title: Structure of lymphostatin, a potent virulence factor from pathogenic Escherichia coli
Authors: Griessmann M / Rasmussen T / Flegler V / Kraft C / Schneider R / Spantzel L / Borsch M / Bottcher B
History
DepositionMar 28, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19984.png

Downloads & links

-
Map

FileDownload / File: emd_19984.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrelion map from Refine3D job, no sharpening
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 378.4 Å		0.95 Å/pix.
x 400 pix.
= 378.4 Å		0.95 Å/pix.
x 400 pix.
= 378.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.013019068 - 0.027752008
Average (Standard dev.)-0.000001882514 (±0.00056536973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 378.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A

Fileemd_19984_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_19984_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Lymphostatin

EntireName: Lymphostatin
Components
  • Complex: Lymphostatin
    • Protein or peptide: Lymphostatin

-
Supramolecule #1: Lymphostatin

SupramoleculeName: Lymphostatin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: C-terminal His6 tag
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)
Molecular weightTheoretical: 300 KDa

-
Macromolecule #1: Lymphostatin

MacromoleculeName: Lymphostatin / type: protein_or_peptide / ID: 1 / Details: C-terminal His6 tag / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLPEKVLFP PVTSGLSGQE KQKKPKSITG FQENYQRNIR PIKTASEARL RFFDKMVSKE NSLEDVVSL GEMIQKEIYG HEQRTFSPVH HTGNWKSSLL HNALLGLANV YNGLRETEYP N TFNRDGIK STNSFRDNLL TKTRTPRDNF EEGIKHPEHA TIPYDNDNES ...String:
MRLPEKVLFP PVTSGLSGQE KQKKPKSITG FQENYQRNIR PIKTASEARL RFFDKMVSKE NSLEDVVSL GEMIQKEIYG HEQRTFSPVH HTGNWKSSLL HNALLGLANV YNGLRETEYP N TFNRDGIK STNSFRDNLL TKTRTPRDNF EEGIKHPEHA TIPYDNDNES NKLLKAGKIA GN NNELLME IKKESQSDHQ IPLSDKFLKR KKRSPVAEDK VQNSLTPENF VQKISLSDEL KTK YANEII EIKRIMGEYN LLPDKNSRNG LKLLQKQADL LKIIMEDTSV TENTFKNIEI AITD IKREY YSHTVDIEKN IHAIWVAGSP PESISDYIKT FLKTYKEFTY YLWVDEKAFG AAKFT SVLK QIAFDLACRT IQQNTPQKNI DFINLYNEIR KKYNNNPSGQ QEYLNKLREL YATYQK IST PLKHMFNSFF LENMIKLQDN FFNYCIVKGV TEINDELRIN YLKNVIKLSD DDIGNYQ KT INDNKDRVKK LILDLQKQFG ENRISIKDVN SLTSLSKSEN NHNYQTEMLL RWNYPAAS D LLRMYILKEH GGIYTDTDMM PAYSKQVIFK IMMQTNGDNR FLEDLKLRRA ISDGVLRYV NNQNIDEVNY NEISDADKNI IKKILTEISK MPEDSIFTKI NTRIPRDTMP ILRRYHLWPD GWNIRGLNG FMLSHKGSEV IDAVIAGQNQ AYRELRRIRD NIHSEIYFKQ TDELSSLPDT D KIGGILVK KYLSGSLFSK FRQDTIIPEA LSTLQISGPD LIQRKMLQFF RSRGVLGEEF IN ERKLSDK AYIGVYKTTG TGKYDWLTPE SIGVNDVTPA DESTWCIGKG RCVDDFLFKD VST LKTENL PELFLTKIDT DTFFSQWSTK TKKDLQKKIQ DLTVRYNELI DSSTIDFKNL YEID QMLHM IMLEMNDDIA KRSLFSLQVQ IAEKIRRMTI PVDNIINIYP DLHKKNDNDL SMSIK GFLA SNPHTKINIL YSNKTEHNIF IKDLFSFAVM ENELRDIINN MSKDKTPENW EGRVML QRY LELKMKDHLS LQSSQEANEF LEISTFIYEN DFLREKIEAV KNKMNSHELY FEKIKKE QN TWQDLSTKEQ KLQLIKALKE ISGNTEKDSH YDRLLDAFFK KHNENIHNKI QRIKDEFK E YSRVAIHNID KVIFKGQTLD RLYHEGYVFS DINTLSRYTL HGLGITGVHT EENLLPAPS SSLINILKEH YNEDEISAKL PLAYDYILNK KESSSIPVEI LNKLSELPPH ELLTPVLGQS VNPLGMGYS SDNGKITEQV IVSGADGFDN PISGLIYTYL EDLYNIHVRM REGTLNSQNL R QLLENSVS SCFLTEQSIN KLLSEAEKRP YQSLTEIHQH LTGLPTIADA TLSLLSVGLP GT GKLLRRE QDYGRPPVTA IQDSTFVLPY NFKGIGFNDN IISSAPVASS LHFIAEHAKY TLL SWPEFY RHHAQRWFEM AKGYGSQNID FHPQSLLVTQ EGRCMGLALL YLQTEDTAHY SILQ ENLMT VSALHQTSNR DKLPLSKDDN SLMTRTYSLI EMLQYQGNKY ITNESLLHKT AWNQE RITL LFNEKGVKRA LISTPNHTLV LQQLEDIYRL TDPNFGHADF LSPIDALKFI EAMIQL TPT LQEYYGLLNK DINKHIQVHY AESDMVWNKL LPENDAGLST RIQHTTTDRL ANLAEPV AV AGISLPVKTL YDIGATLDGR RITSPPTSEQ IPSLRLNGDV LNDYLSRTVL TPEQADNI R KILHTQGIRS GTRPIDPEMI RGTQDDLVSS QTRLQRQATR VKQQLAGVLD TLQQHFQNI PRSSGRHLSV ENIELADIGS GRFNLQIRDG ETLHTTSVEV PEVVSRFQKL STMLSALPAS GIMDFDLGM SVVGVVQYAR LLQQGHEDST LAKINLAMDI KQLSEATLGS MIQIAGNKFL N TEGIQGFR LESAVAEGMR SVATRTGGTM GKALSASARV LELPVLETVL GTWNLYNSVI QL QQATSYS ETMAARVQIA FDSISLGLTA ASVAFPPLII ATGPIAAIGM GASSIARNVA RKE ERHTQW LEYKKFLTDG SKHIVVASPE RGLLDFSGNK VFGKMVLDLR QSPPLLHGES SFNA DRKIG HRPDLGDWQI REKVGYANSI SPYSSLAHGY ANSKWPRTIP KIPSGEYDTI ILGYG HQYQ ANTEIEYLSN WIVWREAVPD STSRHKRPPL EVLNSQCTVI AGERKTTVLP LRVLSD LTP ECTEQAISLK DYKFILRGGS GGLAVQVGGA GYYDIDANLV AKENTLSFRG LPEEFPL TF DLSKQTQSVM LKTPDDEVPV MTITQKGINT LVGTAAGKDR LIGNDKDNTF HTSSGGGT V ISGGGNNRYI IPRDLKTPLT LTLSSNSVSH EIFLPETTLA ELKPVAFELS LIYWAGNNI NVQPEDEAKL NHFAGNFRVH TRDGMTLEAV SRENGIQLAI SLCDVQRWQA VYPEENNRPD AILDRLHDM GWSLTPEVRF QGGETQVSYD PLTRQLVYQL QARYSEFQLA GSRHHTTAVT G TPGSRYII MKPVTTQILP TQIILAGDND HPETIDLLEA SPVLVEGKKD KNSVILTIAT IQ YSLQLTI SGIEESLPET TRVAIQPQDT RLLGDVLRIL PDNGNWVGIF RSGHTPTVNR LEN LMALNQ VMTFLPRVSG SAEQVLCLEN LGGVRKKVEG ELLSGKLKGA WKAEGEPTVP VNIS DLSIP PYSRLYLIFE GKNNVLLRSK VHAAPLKITS AGEMQLSERQ WQQQEHIIVK PDNEA PSLI LSEFRRFTIS SDKTFSLKLM CHQGMVRIDR RSLSVRLFYL REQPGIGSLR LTFRDF FTE VMDTTDREIL EKELRPILIG DTHRFINAAY KNHLNIQLGD GVLNLADIVA EYARIQK EE TSKILYQYQG AMKKKTDGPS VVEDAIMTTT VTTDSGELFP TFHPWYTDDL SGRYKSVP M ARKADTLYHL TPKGDLQIIY QVATKMVNQA MIVSLPNYRH EWEKYNLSIL SEIPQNNNT VVHSILRVNG PTMQVRTIDY RGTDENNPIV SFSDTTFING EQMLSYDSHS SGRVYSREEY MMWELQQRV SEASSARTQD YWLMDAAVRN GEWKITPELL RHTPGYIRST VSKWSRGWLK T GTILQTPE DRNTDVYLTT IQNNVFSRQG GGYQVYYRID GMAGADIADN APGETRCTLR PG TCFEVTS VDERHYEWNI IYVTLKTCGW SRNGQSKTPN GDNLFNHHHH HH

UniProtKB: Efa1/LifA protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.9 mg/mL
BufferpH: 4
Component:
ConcentrationFormulaName
25.0 mMNaH2PO4sodium dihydrongen phosphate
100.0 mMNaClsodium chloride
0.075 mMMnCl2manganese cloride
1.5 mMC9H15O6PHClTCEP
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 41392 / Average exposure time: 6.2 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 13373262
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 627040
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

+
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