+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40056 | |||||||||
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Title | Structure of Trypanosoma docking complex | |||||||||
Map data | This 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 |
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Keywords | Peroxisomal transport / Import / PEX / TRANSPORT PROTEIN / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information protein import into peroxisome matrix, docking / malate dehydrogenase / L-malate dehydrogenase activity / peroxisomal membrane / carboxylic acid metabolic process / tricarboxylic acid cycle / peroxisome Similarity search - Function | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) / Trypanosoma cruzi strain CL Brener (eukaryote) / Trypanosoma cruzi cruzi (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Sonani RR / Artur B / Jemiola-Rzeminska M / Lipinski O / Patel SN / Sood T / Dubin G | |||||||||
Funding support | Poland, 2 items
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Citation | Journal: To Be Published Title: Structure of Trypanosoma docking complex Authors: Sonani RR / Dubin G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40056.map.gz | 3.9 MB | EMDB map data format | |
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Header (meta data) | emd-40056-v30.xml emd-40056.xml | 23 KB 23 KB | Display Display | EMDB header |
Images | emd_40056.png | 85.7 KB | ||
Filedesc metadata | emd-40056.cif.gz | 6.5 KB | ||
Others | emd_40056_additional_1.map.gz emd_40056_additional_2.map.gz emd_40056_additional_3.map.gz emd_40056_half_map_1.map.gz emd_40056_half_map_2.map.gz | 14.5 MB 110.4 MB 200.6 MB 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40056 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40056 | HTTPS FTP |
-Related structure data
Related structure data | 8gi0MC 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_40056.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | This 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. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Component 1 - MDH of coposite map. Separately...
File | emd_40056_additional_1.map | ||||||||||||
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Annotation | Component 1 - MDH of coposite map. Separately depositied to EMBD, EMD-40053 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_40056_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_40056_additional_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40056_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40056_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import
Entire | Name: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import |
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Components |
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-Supramolecule #1: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import
Supramolecule | Name: Docking complex (MDH)4-(Pex5)1-(Pex14)1 of Trypanosoma Pex import type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Trypanosoma cruzi (eukaryote) |
-Macromolecule #1: Peroxisomal membrane protein PEX14
Macromolecule | Name: Peroxisomal membrane protein PEX14 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma cruzi (eukaryote) |
Molecular weight | Theoretical: 40.507551 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: malate dehydrogenase
Macromolecule | Name: malate dehydrogenase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma cruzi strain CL Brener (eukaryote) |
Molecular weight | Theoretical: 34.106832 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 #3: Peroxisome targeting signal 1 receptor
Macromolecule | Name: Peroxisome targeting signal 1 receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Trypanosoma cruzi cruzi (eukaryote) |
Molecular weight | Theoretical: 74.268422 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.25 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 482240 |