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- EMDB-22816: Full-length human mitochondrial Hsp90 (TRAP1) in complex with Sdh... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22816 | |||||||||||||||||||||
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Title | Full-length human mitochondrial Hsp90 (TRAP1) in complex with SdhB in the presence of AMP-PNP | |||||||||||||||||||||
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![]() | Hsp90 / CHAPERONE / TRAP1 / SdhB / mitochondria | |||||||||||||||||||||
Function / homology | ![]() translational attenuation / negative regulation of cellular respiration / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport ...translational attenuation / negative regulation of cellular respiration / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of 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 / ubiquinone binding / proton motive force-driven mitochondrial ATP synthesis / negative regulation of reactive oxygen species biosynthetic process / : / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / cell periphery / ATP-dependent protein folding chaperone / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / unfolded protein binding / protein folding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||||||||||||||
![]() | Liu YX / Agard DA | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.5 KB | Display | ![]() |
Images | ![]() | 98.9 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kcmMC ![]() 7kckC ![]() 7kclC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() |
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: ![]() |
Molecular weight | Theoretical: 74.17757 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() |
Molecular weight | Theoretical: 15.097539 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSAQTAAATA PRIKKFAIYR WDPDKAGDKP HMQTYEVDLN KCGPMVLDAL IKIKNEVDST LTFRRSCREG ICGSCAMNIN GGNTLACTR RIDTNLNKVS KIYPLPHMYV IKDLVPDLSN FYAQYKSIEP YLKKK 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 |
-Macromolecule #6: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ![]() ChemComp-FES: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||
Output model | ![]() PDB-7kcm: |