[English] 日本語
![](img/lk-miru.gif)
- PDB-7kcl: Full-length human mitochondrial Hsp90 (TRAP1) in complex with Sdh... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7kcl | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Full-length human mitochondrial Hsp90 (TRAP1) in complex with SdhB in the presence of AMP-PNP | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | CHAPERONE / Hsp90 / TRAP1 / SdhB / mitochondria | |||||||||||||||||||||
Function / homology | ![]() 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 | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||||||||||||||
![]() | Liu, Y.X. / Agard, D.A. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: Cryo-EM reveals the dynamic interplay between mitochondrial Hsp90 and SdhB folding intermediates Authors: Liu, Y.X. / Agard, D.A. / Elnatan, D. / Sun, M. / Myasnikov, A.G. | |||||||||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 239.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 188 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 45.7 KB | Display | |
Data in CIF | ![]() | 67.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 22812MC ![]() 7kckC ![]() 7kcmC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 74177.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 15251.708 Da / Num. of mol.: 1 / Fragment: UNP residues 29-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Chemical | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: human Trap1 in complex with SdhB in the presence of AMP-PNP Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.162 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software | Name: CTFFIND / Category: CTF correction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236804 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
| ||||||||||||||||||||||||
Refine LS restraints |
|