[English] 日本語
Yorodumi- EMDB-22177: Human mitochondrial Hsp90 (TRAP1) NTD-Middle domain dimer with AD... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22177 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human mitochondrial Hsp90 (TRAP1) NTD-Middle domain dimer with ADP-BeF3 | |||||||||
Map data | Hsp90 (TRAP1) NTD-Middle domain dimer with ADP-BeF3 | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.11 Å | |||||||||
Authors | Liu YX / Wang F / Agard DA | |||||||||
Funding support | United States, 2 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22177.map.gz | 60 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22177-v30.xml emd-22177.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22177_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_22177.png | 71.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22177 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22177 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_22177.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Hsp90 (TRAP1) NTD-Middle domain dimer with ADP-BeF3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Trap1 dimer with ADP-BeF3
Entire | Name: Trap1 dimer with ADP-BeF3 |
---|---|
Components |
|
-Supramolecule #1: Trap1 dimer with ADP-BeF3
Supramolecule | Name: Trap1 dimer with ADP-BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 147 KDa |
-Macromolecule #1: human mitochondrial Hsp90 (TRAP1)
Macromolecule | Name: human mitochondrial Hsp90 (TRAP1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA ...String: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA PGSLGYQWLS DGSGVFEIAE ASGVRTGTKI IIHLKSDCKE FSSEARVRDV VTKYSNFVSF PLYLNGRRMN TLQAIWMMDP KDVGEWQHEE FYRYVAQAHD KPRYTLHYKT DAPLNIRSIF YVPDMKPSMF DVSRELGSSV ALYSRKVLIQ TKATDILPKW LRFIRGVVDS EDIPLNLSRE LLQESALIRK LRDVLQQRLI KFFIDQSKKD AEKYAKFFED YGLFMREGIV TATEQEVKED IAKLLRYESS ALPSGQLTSL SEYASRMRAG TRNIYYLCAP NRHLAEHSPY YEAMKKKDTE VLFCFEQFDE LTLLHLREFD KKKLISVETD IVVDHYKEEK FEDRSPAAEC LSEKETEELM AWMRNVLGSR VTNVKVTLRL DTHPAMVTVL EMGAARHFLR MQQLAKTQEE RAQLLQPTLE INPRHALIKK LNQLRASEPG LAQLLVDQIY ENAMIAAGLV DDPRAMVGRL NELLVKALER HGGSGSGSSA MVDTLSGLSS EQGQSGDMTI EEDSATHIKF SKRDEDGKEL AGATMELRDS SGKTISTWIS DGQVKDFYLY PGKYTFVETA APDGYEVATA ITFTVNEQGQ VTVNGKATKG DAHI |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 74.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|