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- EMDB-40056: Structure of Trypanosoma docking complex -

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Basic information

Entry
Database: EMDB / ID: EMD-40056
TitleStructure of Trypanosoma docking complex
Map dataThis is main composite map, generated from two component maps. Component 1 - MDH_flipped.mrc and Component 2 - PEX_fliiped.mrc, which are provided as additional maps.
Sample
  • Complex: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import
    • Protein or peptide: Peroxisomal membrane protein PEX14
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor
KeywordsPeroxisomal transport / Import / PEX / TRANSPORT PROTEIN / PROTEIN TRANSPORT
Function / homology
Function and homology information


intracellular organelle lumen / peroxisome matrix targeting signal-1 binding / peroxisomal importomer complex / protein import into peroxisome matrix, docking / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / peroxisomal membrane / tricarboxylic acid cycle / signaling receptor binding ...intracellular organelle lumen / peroxisome matrix targeting signal-1 binding / peroxisomal importomer complex / protein import into peroxisome matrix, docking / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / peroxisomal membrane / tricarboxylic acid cycle / signaling receptor binding / cytoplasm / cytosol
Similarity search - Function
Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / 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 ...Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Peroxisomal membrane protein PEX14 / malate dehydrogenase / Peroxisome targeting signal 1 receptor
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote) / Trypanosoma cruzi strain CL Brener (eukaryote) / Trypanosoma cruzi cruzi (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 Centre2020/39/B/NZ1/01551 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 13, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40056.png

Downloads & links

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Map

FileDownload / File: emd_40056.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is main composite map, generated from two component maps. Component 1 - MDH_flipped.mrc and Component 2 - PEX_fliiped.mrc, which are provided as additional maps.
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: 0.13
Minimum - Maximum-2.347877 - 3.7117522
Average (Standard dev.)0.0006050513 (±0.040152363)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: Component 1 - MDH of coposite map. Separately...

Fileemd_40056_additional_1.map
AnnotationComponent 1 - MDH of coposite map. Separately depositied to EMBD, EMD-40053
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_40056_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_40056_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40056_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40056_half_map_2.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import

EntireName: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import
Components
  • Complex: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import
    • Protein or peptide: Peroxisomal membrane protein PEX14
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: Peroxisome targeting signal 1 receptor

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Supramolecule #1: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import

SupramoleculeName: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi (eukaryote)

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Macromolecule #1: Peroxisomal membrane protein PEX14

MacromoleculeName: Peroxisomal membrane protein PEX14 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Molecular weightTheoretical: 40.507551 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNTATTVGVT GDGDARQRNS PEESEKRKRV SSAVQFLHDS RVKITPAANK IQFLKSKGLT TEEVCEAFEK AGQTIPLDEI KKIMNKPSF GQLGSGVVNN NLAPGHVGSD ATYVLRQHPF MPHAGPLYTQ QPPPFPQTPQ GAKETDWRDV IIGVGAALIS G FAAFKAFQ ...String:
MNTATTVGVT GDGDARQRNS PEESEKRKRV SSAVQFLHDS RVKITPAANK IQFLKSKGLT TEEVCEAFEK AGQTIPLDEI KKIMNKPSF GQLGSGVVNN NLAPGHVGSD ATYVLRQHPF MPHAGPLYTQ QPPPFPQTPQ GAKETDWRDV IIGVGAALIS G FAAFKAFQ IYSPYEIRRK DERTKKGSRM ESQRRGKRHE GSVSPDRGAE RPVTSLHTMA PPMPATPTPL PTATAANAAE ST EREIQKL QSELKETQEA LEKEKRSKAE ISVSLGKLRG QINALSRTND NLESRIKLLQ EEVDKANSEA NKRKELDASF TGA ADGVPK SQSEDAIQPN GPPLLTPKIL ADTVGCNSAA LNELPVLTAV EFVPEE

UniProtKB: Peroxisomal membrane protein PEX14

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Macromolecule #2: malate dehydrogenase

MacromoleculeName: malate dehydrogenase / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Peroxisome targeting signal 1 receptor

MacromoleculeName: Peroxisome targeting signal 1 receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma cruzi cruzi (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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 482240
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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