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Yorodumi- EMDB-22812: Full-length human mitochondrial Hsp90 (TRAP1) in complex with Sdh... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22812 | |||||||||||||||||||||
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Title | Full-length human mitochondrial Hsp90 (TRAP1) in complex with SdhB in the presence of AMP-PNP | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Keywords | Hsp90 / CHAPERONE / TRAP1 / SdhB / mitochondria | |||||||||||||||||||||
Function / homology | Function and homology information translational attenuation / negative regulation of cellular respiration / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide ...translational attenuation / negative regulation of cellular respiration / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / 3 iron, 4 sulfur cluster binding / proton motive force-driven mitochondrial ATP synthesis / ubiquinone binding / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / cell periphery / mitochondrial membrane / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / unfolded protein binding / protein folding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||||||||||||||
Authors | Liu YX / Agard DA | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: To Be Published Title: Cryo-EM reveals the dynamic interplay between mitochondrial Hsp90 and SdhB folding intermediates Authors: Liu YX / Agard DA / Elnatan D / Sun M / Myasnikov AG | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22812.map.gz | 116.9 MB | EMDB map data format | |
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Header (meta data) | emd-22812-v30.xml emd-22812.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22812_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_22812.png | 108.9 KB | ||
Filedesc metadata | emd-22812.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22812 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22812 | HTTPS FTP |
-Validation report
Summary document | emd_22812_validation.pdf.gz | 596.8 KB | Display | EMDB validaton report |
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Full document | emd_22812_full_validation.pdf.gz | 596.3 KB | Display | |
Data in XML | emd_22812_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_22812_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22812 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22812 | HTTPS FTP |
-Related structure data
Related structure data | 7kclMC 7kckC 7kcmC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22812.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.814 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human Trap1 in complex with SdhB in the presence of AMP-PNP
Entire | Name: human Trap1 in complex with SdhB in the presence of AMP-PNP |
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Components |
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-Supramolecule #1: human Trap1 in complex with SdhB in the presence of AMP-PNP
Supramolecule | Name: human Trap1 in complex with SdhB in the presence of AMP-PNP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 162 KDa |
-Macromolecule #1: Heat shock protein 75 kDa, mitochondrial
Macromolecule | Name: Heat shock protein 75 kDa, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 74.17757 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS ...String: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS AAPGSLGYQW LSDGSGVFEI AEASGVRTGT KIIIHLKSDC KEFSSEARVR DVVTKYSNFV SFPLYLNGRR MN TLQAIWM MDPKDVGEWQ HEEFYRYVAQ AHDKPRYTLH YKTDAPLNIR SIFYVPDMKP SMFDVSRELG SSVALYSRKV LIQ TKATDI LPKWLRFIRG VVDSEDIPLN LSRELLQESA LIRKLRDVLQ QRLIKFFIDQ SKKDAEKYAK FFEDYGLFMR EGIV TATEQ EVKEDIAKLL RYESSALPSG QLTSLSEYAS RMRAGTRNIY YLCAPNRHLA EHSPYYEAMK KKDTEVLFCF EQFDE LTLL HLREFDKKKL ISVETDIVVD HYKEEKFEDR SPAAECLSEK ETEELMAWMR NVLGSRVTNV KVTLRLDTHP AMVTVL EMG AARHFLRMQQ LAKTQEERAQ LLQPTLEINP RHALIKKLNQ LRASEPGLAQ LLVDQIYENA MIAAGLVDDP RAMVGRL NE LLVKALERH UniProtKB: Heat shock protein 75 kDa, mitochondrial |
-Macromolecule #2: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitocho...
Macromolecule | Name: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.251708 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGSAQTAAA TAPRIKKFAI YRWDPDKAGD KPHMQTYEVD LNKCGPMVLD ALIKIKNEVD STLTFRRSCR EGICGSCAMN INGGNTLAC TRRIDTNLNK VSKIYPLPHM YVIKDLVPDL SNFYAQYKSI EPYLKKK UniProtKB: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial |
-Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-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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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 72.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||
Output model | PDB-7kcl: |