[English] 日本語
Yorodumi
- EMDB-16257: Cryo-EM structure of Toxoplasma gondii glideosome-associated connector -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16257
TitleCryo-EM structure of Toxoplasma gondii glideosome-associated connector
Map data
Sample
  • Complex: toxoplasma gondii glideosome-associated connector
    • Protein or peptide: toxoplasma gondii glideosome-associated connector
Keywordsactin-binding protein / armadillo repeat / solenoid / pleckstrin-homology domain / PROTEIN BINDING
Biological speciesToxoplasma gondii (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsChen Q / Rosenthal P
Funding support Finland, Norway, United Kingdom, 7 items
OrganizationGrant numberCountry
Academy of Finland Finland
Sigrid Juselius Foundation Finland
Jane and Aatos Erkko Foundation Finland
Norwegian Research Council Norway
Wellcome TrustCC2106 United Kingdom
Cancer Research UKCC2106 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2106 United Kingdom
CitationJournal: To Be Published
Title: Structure of Toxoplasma gondii glideosome-associated connector suggests a role as an elastic element to assist myosin A in generating force for gliding motility
Authors: Hung YF / Chen Q / Pires I / Rosenthal P / Kursula I
History
DepositionDec 2, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16257.png

Downloads & links

-
Map

FileDownload / File: emd_16257.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.61 Å/pix.
x 200 pix.
= 322. Å		1.61 Å/pix.
x 200 pix.
= 322. Å		1.61 Å/pix.
x 200 pix.
= 322. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.61 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.04
Minimum - Maximum-3.6586165 - 6.96944
Average (Standard dev.)-0.007352429 (±0.20886381)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16257_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16257_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16257_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : toxoplasma gondii glideosome-associated connector

EntireName: toxoplasma gondii glideosome-associated connector
Components
  • Complex: toxoplasma gondii glideosome-associated connector
    • Protein or peptide: toxoplasma gondii glideosome-associated connector

-
Supramolecule #1: toxoplasma gondii glideosome-associated connector

SupramoleculeName: toxoplasma gondii glideosome-associated connector / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Toxoplasma gondii (eukaryote)

-
Macromolecule #1: toxoplasma gondii glideosome-associated connector

MacromoleculeName: toxoplasma gondii glideosome-associated connector / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: G(MSE)AIGKVKRN PDAGVATAVQ SVIQHQTFKR (MSE)LLFGLRSLA DFCSPSNQLY QENALDALDR GVLSAIQTAV TT FSDDDDL (MSE)LCASRVLWA (MSE)SVAIKEE(MSE)D PAHIARVHSE GSPVIVAVVN SSPTDPQTIE DS(MSE)NFVD NL KRAGAPVDGA ...String:
G(MSE)AIGKVKRN PDAGVATAVQ SVIQHQTFKR (MSE)LLFGLRSLA DFCSPSNQLY QENALDALDR GVLSAIQTAV TT FSDDDDL (MSE)LCASRVLWA (MSE)SVAIKEE(MSE)D PAHIARVHSE GSPVIVAVVN SSPTDPQTIE DS(MSE)NFVD NL KRAGAPVDGA SLAGG(MSE)LSIF TKTALD(MSE)KTA KRVTAALAIA AETAEGSTAL YNAGGTSVLL TYCLDQGDLS DAGVE(MSE)VEG AFDTVRY(MSE)AG YQCTDATTLP QCIAL(MSE)DKYR GRKSASAKGS SALAA(MSE)IGPE QLQKC LNTL KTAEAGSAEY DEALVTLGS(MSE) SYISSFTDEI VRAGGVPLLI ELINSGLPQ(MSE) EGNPEKIAS(MSE) ISGA AK(MSE)LA RIASNPVNVD AIVQAGGVAT LCTAVSYCTE S(MSE)EALGALC(MSE) ALVPLASRES LAHEIVQYQT FAT VLPILY QNVESPEIAA LA(MSE)ELVATGS QHEEIQEH(MSE)L QNQAAEICSL CCQYHTADAS YQQHAISALN RLVPRL TTL HGVSEYGGIQ GVIASLNANV NNEQVALLAV QLLDNFSEVS DAKTY(MSE)SDGT CVDAVLAA(MSE)L EHEGNDLLI SAGVHCLARI ATEDDCARHL NVLDTAIQTA RGNPDGVYRV LAAISGLSRV PSLRQIFEEK NASDTILAGI SSWIECSRFE GQNRIIKAA LKTVKN(MSE)KIS GDGDLTSCFA A(MSE)CDVACLPQ VKRVVELEEP DNNILVADTA AFRDLAAT(MSE) RITGAENLER CIESVLRV(MSE)R KYPDSRRAQL NCLETLNYLA QCDGGEGVAI LSRTGGLNAV VQYLTRAP(MSE)Y LD AQIAGFT VLATSAKIDS NVGETLRKCN CLQALKVA(MSE)R THAKSKELKR TIAPLVALL(MSE) PTDALETEIQ ELLNE CASA CEKNNFPHLH ENLAALNELL ISSEGAKIAA RLGIGAH(MSE)CK YQEYISAHEQ DALAVTDYDI LGKDLFDATV SE CAHA(MSE)EQ VASTRSGRNA LIKAGNVATL ISLYESLKAP QSQYSEEAAI HCLEALRILL KSDKRSAELA FERNFVSTL CVGIDSFPHS APVLGATCAC LAA(MSE)ATTPER VQ(MSE)LTAQPAF ESLLQKLVFV IQNDPSKDNK LVA(MSE)RALQ E LVEITNDAT(MSE) ANKIAEAGAV TALFRIIDEY GDDEQLTVQA AEVLALLGAF EDLRRFYDND VRFPAQVLTA ALTKQ KNNE TAVVHLLDVL NKLATSEDRA VLRELGV(MSE)EQ VADA(MSE)RVHSE SEAVTRLGGE LFAK(MSE)GADEQ IKSL (MSE)LQII ETVESGAEDT AQTVDILCGR LAVFLAAPLE DPRDALQHTE KCLGSLVATL QTYPGSERLE GNVALVCRRL C DRCFDDAD DPYGAWAVAA SG(MSE)LAQFAG(MSE) VAGETVLANK KFLGPAYRTF TACCANAYC(MSE) PT(MSE)VEV APS FLPQTYTLLE (MSE)HKNDAETVA RVLEFLRYFA EDPTACGLIV QN(MSE)SGSSGDV VALTVLL(MSE)QQ HQNND AVVC AG(MSE)EFLGALA YTLSQAGYEP LPTLADGSVL RDCDAL(MSE)GSN SSSARQLAH(MSE) H(MSE)IEK(MSE) LLS KAYNDALIQE QALKKLT(MSE)SL KAEDDKKRFS DEERAGLYAA (MSE)ACVLLAAGG AGLTGE(MSE)EKF NGFEV VLQA IEEFGENPTV IKEVNRALQG LS(MSE)ADVN(MSE)TA RTVKEAVPKL CTEATTAIQT DAECADTFCD L(MSE)LQ LVSQE GNGRQLLQVY GLEETLQGVE NLAAYYGEDF GTQLSEKVA(MSE) IRQA(MSE)EDDQP REKTCKDVYD LLNSRVQ QG LSVAISEVAI LQEEVEFLVS Q(MSE)G(MSE)YNQEQL DHQTA(MSE)GADH QYGN(MSE)AFELL AATSANVKLL QA NEFSK(MSE)E LALIKGQADP EIVLYAVKAL TAFCKFPPAA QDTARIQGCP ALVTEACSKI NKSGLPNERK EEHLCARYF LVERTAINRN LYNKTPI(MSE)TE LINSWNDYDK GAYTTTLLRF VFRA(MSE)RRVVS DAHVEELLKA NVLQRLIGII SD VNAD(MSE)AL LPDVLFLLGS LAVVPEIKTK IGELNGIAAC TDLLQRALPK PNTAPVVTNV CLAFANICIG HKKNTEIFS KLGGPALNVK VLNDRGHEYD VCNAASVLLC NLLYKNES(MSE)K KLLGTNGAPA ALVKGLSNYD GSEEKTAIRC LESVFK AIS NLSLYTPNIQ PFLDAGIENA YSTWLSNLSE TFPDAQLETG CRTLVNLV(MSE)E NEENN(MSE)RKFG VCLLPC (MSE)AV AKQGRTDTKA LLLLLDIEAS LCRLKENAEA FAANGGIETT IRLIHQFDYD VGLLTLGIHL LGIQSAVKDS IQR (MSE)(MSE)DADV FSILVGCVEV DAEGNEVTDL VVGGLRCTRR IVRSEELAFE YCNAGGIATI ANVICKSINQ P(MSE) V(MSE)LEACR VLLGLLFYTT RSQADRQAAV EALHAQCQQR AEQ(MSE)HAQAQA DYEAGVVSEP PPEE(MSE)EVPEP D PDELANAA YGGWYQ(MSE)G(MSE)D EV(MSE)IDAILQA VCACAAVEAH AKQLRLQRVC LGLAAYFASE Q(MSE)GTSS LVG SGIEQVLTQI (MSE)TNFAGEGTT (MSE)QLSCVIINS IA(MSE)TSGD(MSE)YE EIKTSALLSA LKTSVGK (MSE)A TKKPEEKALK ETCAATLEAA SSGEDPFDAF SKTVTELDFK FTEWNVDPYP NGVHDLPSNV KEALRKGGKL KVFL PEKEK EEIRWRSSQD LNVFEWC(MSE)GN DQDYNNRIPI VRIRNVAKGL VHPALKAAAK KEPRKVAAKF T(MSE)CLFGP PN DDFPEGVELP (MSE)VAKSQKERD AFVE(MSE)(MSE)VQWR DAATYNFHHH HHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8bt6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69523
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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