[English] 日本語
Yorodumi
- EMDB-50340: Cryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50340
TitleCryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex
Map data
Sample
  • Complex: Ternary complex of (MDH)4 with PEX5
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor
KeywordsPeroxisomal protein transport / Cargo-Receptor complex / TRANSPORT PROTEIN
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / peroxisome
Similarity search - Function
PEX5/PEX5L / Malate dehydrogenase, type 1 / Tetratricopeptide repeat / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / TPR repeat region circular profile. ...PEX5/PEX5L / Malate dehydrogenase, type 1 / Tetratricopeptide repeat / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
malate dehydrogenase / Peroxisome targeting signal 1 receptor
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLipinski O / Sonani RR / Blat A / Jemiola-Rzeminska M / Patel SN / Sood T / Dubin G
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: To Be Published
Title: Cryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex
Authors: Lipinski O / Sonani RR / Blat A / Jemiola-Rzeminska M / Patel SN / Sood T / Dubin G
History
DepositionMay 19, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50340.png

Downloads & links

-
Map

FileDownload / File: emd_50340.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.0809
Minimum - Maximum-1.1485864 - 1.7755129
Average (Standard dev.)0.00048992666 (±0.043927714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 248.64 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_50340_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_50340_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of (MDH)4 with PEX5

EntireName: Ternary complex of (MDH)4 with PEX5
Components
  • Complex: Ternary complex of (MDH)4 with PEX5
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor

-
Supramolecule #1: Ternary complex of (MDH)4 with PEX5

SupramoleculeName: Ternary complex of (MDH)4 with PEX5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 231 KDa

-
Macromolecule #1: malate dehydrogenase

MacromoleculeName: malate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: malate dehydrogenase
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 35.13798 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHMV NVAVIGAAGG IGQSLSLLLL RELPFGSTLS LYDVVGAPGV AADLSHIDRA GITVKHAAGK LPPVPRDPAL TELAEGVDV FVIVAGVPRK PGMTRDDLFN VNAGIVMDLV LTCASVSPNA CFCIVTNPVN STTPIAAQTL RKIGVYNKNK L LGVSLLDG ...String:
MAHHHHHHMV NVAVIGAAGG IGQSLSLLLL RELPFGSTLS LYDVVGAPGV AADLSHIDRA GITVKHAAGK LPPVPRDPAL TELAEGVDV FVIVAGVPRK PGMTRDDLFN VNAGIVMDLV LTCASVSPNA CFCIVTNPVN STTPIAAQTL RKIGVYNKNK L LGVSLLDG LRATRFINNA RHPLVVPYVP VVGGHSDVTI VPLYSQIPGP LPDESTLKEI RKRVQVAGTE VVKAKAGRGS AT LSMAEAG ARFTMHVVKA LMGLDTPMVY AYVDTDGEHE CPFLAMPVVL GKNGIERRLP IGPITTVEKE MLEEAVGVVK KNI AKGETF ARSKL

UniProtKB: malate dehydrogenase

-
Macromolecule #2: Peroxisome targeting signal 1 receptor

MacromoleculeName: Peroxisome targeting signal 1 receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 75.299586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHMD CSTGAAIGQQ FAKDAFHMHG GVGVGPTGNS EHDVLMNEMM MVQTPTGPAG EWTHQFAAYQ GQQQQQQQQH PQELAMRHQ QNDAFMLRQQ QEMEEAFCTF CTTHPHSHAH SHQPQGLVGP AMMGPQIMPP MMFGPGTGGF MMGAPPMMPY A SMKFAGDA ...String:
MAHHHHHHMD CSTGAAIGQQ FAKDAFHMHG GVGVGPTGNS EHDVLMNEMM MVQTPTGPAG EWTHQFAAYQ GQQQQQQQQH PQELAMRHQ QNDAFMLRQQ QEMEEAFCTF CTTHPHSHAH SHQPQGLVGP AMMGPQIMPP MMFGPGTGGF MMGAPPMMPY A SMKFAGDA AMAAANNTNM TQGATATSTT SVQQELQQQS SDNGWVEKLR DAEWAQDYSD AQVFTLEGQS EQTMEEHAKN SE FYQFMDK IRSKELLIDE ETGQLVQGPG PDPDAPEDAE YLKEWAAAEG LNMPPGFFEH MMQRPQGNNE QAEGRLFDGS NDA LMDDGA LDNAADVEEW VREYAEAQEQ LQRVQNETNY PFEPNNPYMY HDKPMEEGIA MLQLANMAEA ALAFEAVCQK EPEN VEAWR RLGTTQAENE KDCLAIIALN HARMLDPKDI AVHAALAVSH TNEHNVGAAL QSLRSWLLSQ PQYEHLGLVD LREVA ADEG LDEVPEENYF FAAPSEYRDC CTLLYAAVEM NPNDPQLHAS LGVLHNLSHR FDEAAKNFRR AVELRPDDAH MWNKLG ATL ANGNRPQEAL EAYNRALDIN PGYVRVMYNM AVSYSNMAQY PLAAKHITRA IALQAGGTNP QGEGSRIATR GLWDLLR MT LNLMDRSDLV EASWQQDLTP FLREFGLEEM AV

UniProtKB: Peroxisome targeting signal 1 receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.79 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.38 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

8ggh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 538505
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://pdbjlvh1.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