[English] 日本語
Yorodumi
- EMDB-40031: Structure of Trypanosoma (MDH)4-(Pex5)2, close conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40031
TitleStructure of Trypanosoma (MDH)4-(Pex5)2, close conformation
Map data
Sample
  • Complex: Complex of MDH-tetramer and PEX5
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor
KeywordsPeroxisomal transport / Trypanosoma / Import / PEX / TRANSPORT PROTEIN
Function / homology
Function and homology information


peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / peroxisomal membrane / tricarboxylic acid cycle / cytosol / cytoplasm
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: 3.66 Å
AuthorsSonani RR / Artur B / Jemiola-Rzeminska M / Lipinski O / 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: Biorxiv / Year: 2023
Title: Noncanonical interactions and conformational dynamics in cargo-Pex5-Pex14 ternary complex for peroxisomal import
Authors: Sonani RR / Blat A / Jemiola-Rzeminska M / Lipinski O / Patel SN / Sood T / Dubin G
History
DepositionMar 9, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40031.png

Downloads & links

-
Map

FileDownload / File: emd_40031.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.29243618 - 0.5527511
Average (Standard dev.)-0.00014523562 (±0.017324883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_40031_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40031_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of MDH-tetramer and PEX5

EntireName: Complex of MDH-tetramer and PEX5
Components
  • Complex: Complex of MDH-tetramer and PEX5
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor

-
Supramolecule #1: Complex of MDH-tetramer and PEX5

SupramoleculeName: Complex of MDH-tetramer and PEX5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)

-
Macromolecule #1: malate dehydrogenase

MacromoleculeName: malate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 34.106832 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVNVAVIGAA GGIGQSLSLL LLRELPFGST LSLYDVVGAP GVAADLSHID RAGITVKHAA GKLPPVPRDP ALTELAEGVD VFVIVAGVP RKPGMTRDDL FNVNAGIVMD LVLTCASVSP NACFCIVTNP VNSTTPIAAQ TLRKIGVYNK NKLLGVSLLD G LRATRFIN ...String:
MVNVAVIGAA GGIGQSLSLL LLRELPFGST LSLYDVVGAP GVAADLSHID RAGITVKHAA GKLPPVPRDP ALTELAEGVD VFVIVAGVP RKPGMTRDDL FNVNAGIVMD LVLTCASVSP NACFCIVTNP VNSTTPIAAQ TLRKIGVYNK NKLLGVSLLD G LRATRFIN NARHPLVVPY VPVVGGHSDV TIVPLYSQIP GPLPDESTLK EIRKRVQVAG TEVVKAKAGR GSATLSMAEA GA RFTMHVV KALMGLDTPM VYAYVDTDGE HECPFLAMPV VLGKNGIERR LPIGPITTVE KEMLEEAVGV VKKNIAKGET FAR SKL

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi strain CL Brener (eukaryote)
Molecular weightTheoretical: 74.268422 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDCSTGAAIG QQFAKDAFHM HGGVGVGPTG NSEHDVLMNE MMMVQTPTGP AGEWTHQFAA YQGQQQQQQQ QHPQELAMRH QQNDAFMLR QQQEMEEAFC TFCTTHPHSH AHSHQPQGLV GPAMMGPQIM PPMMFGPGTG GFMMGAPPMM PYASMKFAGD A AMAAANNT ...String:
MDCSTGAAIG QQFAKDAFHM HGGVGVGPTG NSEHDVLMNE MMMVQTPTGP AGEWTHQFAA YQGQQQQQQQ QHPQELAMRH QQNDAFMLR QQQEMEEAFC TFCTTHPHSH AHSHQPQGLV GPAMMGPQIM PPMMFGPGTG GFMMGAPPMM PYASMKFAGD A AMAAANNT NMTQGATATS TTSVQQELQQ QSSDNGWVEK LRDAEWAQDY SDAQVFTLEG QSEQTMEEHA KNSEFYQFMD KI RSKELLI DEETGQLVQG PGPDPDAPED AEYLKEWAAA EGLNMPPGFF EHMMQRPQGN NEQAEGRLFD GSNDALMDDG ALD NAADVE EWVREYAEAQ EQLQRVQNET NYPFEPNNPY MYHDKPMEEG IAMLQLANMA EAALAFEAVC QKEPENVEAW RRLG TTQAE NEKDCLAIIA LNHARMLDPK DIAVHAALAV SHTNEHNVGA ALQSLRSWLL SQPQYEHLGL VDLREVAADE GLDEV PEEN YFFAAPSEYR DCCTLLYAAV EMNPNDPQLH ASLGVLHNLS HRFDEAAKNF RRAVELRPDD AHMWNKLGAT LANGNR PQE ALEAYNRALD INPGYVRVMY NMAVSYSNMA QYPLAAKHIT RAIALQAGGT NPQGEGSRIA TRGLWDLLRM TLNLMDR SD LVEASWQQDL TPFLREFGLE EMAV

UniProtKB: Peroxisome targeting signal 1 receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.25 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: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12276
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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