+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22174 | |||||||||||||||||||||
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Title | Full-length human mitochondrial Hsp90 (TRAP1) with ADP-BeF3 | |||||||||||||||||||||
Map data | Hsp90 (TRAP1) with ADP-BeF3 | |||||||||||||||||||||
Sample |
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Keywords | Hsp90 / CHAPERONE | |||||||||||||||||||||
Function / homology | Function and homology information translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space ...translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Streptococcus pyogenes (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Liu YX / Wang F | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Authors: Feng Wang / Yanxin Liu / Zanlin Yu / Sam Li / Shengjie Feng / Yifan Cheng / David A Agard / Abstract: Affinity grids have great potential to facilitate rapid preparation of even quite impure samples in single-particle cryo-electron microscopy (EM). Yet despite the promising advances of affinity grids ...Affinity grids have great potential to facilitate rapid preparation of even quite impure samples in single-particle cryo-electron microscopy (EM). Yet despite the promising advances of affinity grids over the past decades, no single strategy has demonstrated general utility. Here we chemically functionalize cryo-EM grids coated with mostly one or two layers of graphene oxide to facilitate affinity capture. The protein of interest is tagged using a system that rapidly forms a highly specific covalent bond to its cognate catcher linked to the grid via a polyethylene glycol (PEG) spacer. Importantly, the spacer keeps particles away from both the air-water interface and the graphene oxide surface, protecting them from potential denaturation and rendering them sufficiently flexible to avoid preferential sample orientation concerns. Furthermore, the PEG spacer successfully reduces nonspecific binding, enabling high-resolution reconstructions from a much cruder lysate sample. | |||||||||||||||||||||
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_22174.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-22174-v30.xml emd-22174.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22174_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_22174.png | 62 KB | ||
Masks | emd_22174_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-22174.cif.gz | 6.1 KB | ||
Others | emd_22174_half_map_1.map.gz emd_22174_half_map_2.map.gz | 98.8 MB 98.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22174 | HTTPS FTP |
-Validation report
Summary document | emd_22174_validation.pdf.gz | 979.3 KB | Display | EMDB validaton report |
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Full document | emd_22174_full_validation.pdf.gz | 978.8 KB | Display | |
Data in XML | emd_22174_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_22174_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22174 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22174 | HTTPS FTP |
-Related structure data
Related structure data | 6xg6MC M: atomic model generated by this map C: citing same article (ref.) |
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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_22174.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Hsp90 (TRAP1) with ADP-BeF3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_22174_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Hsp90 (TRAP1) with ADP-BeF3
File | emd_22174_half_map_1.map | ||||||||||||
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Annotation | Hsp90 (TRAP1) with ADP-BeF3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Hsp90 (TRAP1) with ADP-BeF3
File | emd_22174_half_map_2.map | ||||||||||||
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Annotation | Hsp90 (TRAP1) with ADP-BeF3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trap1 dimer with ADP-BeF3
Entire | Name: Trap1 dimer with ADP-BeF3 |
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Components |
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-Supramolecule #1: Trap1 dimer with ADP-BeF3
Supramolecule | Name: Trap1 dimer with ADP-BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 147 KDa |
-Macromolecule #1: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding pro...
Macromolecule | Name: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptococcus pyogenes (bacteria) |
Molecular weight | Theoretical: 87.094617 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 LLVKALERHG GSGSGSSAMV DTLSGLSSEQ GQSGDMTIEE DSATHIKFSK RDEDGKELAG ATMELRDSSG KTISTWIS D GQVKDFYLYP GKYTFVETAA PDGYEVATAI TFTVNEQGQV TVNGKATKGD AHI UniProtKB: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #3: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-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 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY |
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: 69.0 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
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6xg6: |