+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50340 | |||||||||
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Title | Cryo-EM structure of Trypanosoma cruzi (MDH)4-PEX5 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Peroxisomal protein transport / Cargo-Receptor complex / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Trypanosoma cruzi strain CL Brener (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | |||||||||
Authors | Lipinski O / Sonani RR / Blat A / Jemiola-Rzeminska M / Patel SN / Sood T / Dubin G | |||||||||
Funding support | Poland, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50340.map.gz | 93.3 MB | EMDB map data format | |
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Header (meta data) | emd-50340-v30.xml emd-50340.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_50340.png | 133.3 KB | ||
Filedesc metadata | emd-50340.cif.gz | 5.8 KB | ||
Others | emd_50340_half_map_1.map.gz emd_50340_half_map_2.map.gz | 91.8 MB 91.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50340 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50340 | HTTPS FTP |
-Validation report
Summary document | emd_50340_validation.pdf.gz | 867.5 KB | Display | EMDB validaton report |
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Full document | emd_50340_full_validation.pdf.gz | 867 KB | Display | |
Data in XML | emd_50340_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_50340_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50340 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50340 | HTTPS FTP |
-Related structure data
Related structure data | 9fefMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50340.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_50340_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50340_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of (MDH)4 with PEX5
Entire | Name: Ternary complex of (MDH)4 with PEX5 |
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Components |
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-Supramolecule #1: Ternary complex of (MDH)4 with PEX5
Supramolecule | Name: Ternary complex of (MDH)4 with PEX5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Trypanosoma cruzi strain CL Brener (eukaryote) |
Molecular weight | Theoretical: 231 KDa |
-Macromolecule #1: malate dehydrogenase
Macromolecule | Name: malate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: malate dehydrogenase |
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Source (natural) | Organism: Trypanosoma cruzi strain CL Brener (eukaryote) |
Molecular weight | Theoretical: 35.13798 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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
Macromolecule | Name: Peroxisome targeting signal 1 receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma cruzi strain CL Brener (eukaryote) |
Molecular weight | Theoretical: 75.299586 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.79 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 538505 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |