[English] 日本語
Yorodumi- EMDB-11189: Structure of human mitochondrial HSPD1 as an inverted double ring -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11189 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human mitochondrial HSPD1 as an inverted double ring | |||||||||
Map data | sharpened, final map | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / chaperonin ATPase / Mitochondrial protein import / positive regulation of macrophage activation / cellular response to interleukin-7 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / sperm plasma membrane / B cell activation / DNA replication origin binding / B cell proliferation / apoptotic mitochondrial changes / positive regulation of interferon-alpha production / apolipoprotein binding / positive regulation of interleukin-10 production / protein maturation / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / isomerase activity / sperm midpiece / response to cold / positive regulation of interleukin-12 production / T cell activation / secretory granule / lipopolysaccharide binding / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of T cell activation / unfolded protein binding / positive regulation of type II interferon production / p53 binding / protein folding / single-stranded DNA binding / double-stranded RNA binding / protein-folding chaperone binding / protein refolding / mitochondrial inner membrane / protein stabilization / early endosome / mitochondrial matrix / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Klebl DP / Feasey MC / Muench SP | |||||||||
Funding support | United Kingdom, 2 items
| |||||||||
Citation | Journal: iScience / Year: 2021 Title: Cryo-EM structure of human mitochondrial HSPD1. Authors: David P Klebl / Matthew C Feasey / Emma L Hesketh / Neil A Ranson / Heiko Wurdak / Frank Sobott / Robin S Bon / Stephen P Muench / Abstract: Chaperonins play an important role in folding newly synthesized or translocated proteins in all organisms. The bacterial chaperonin GroEL has served as a model system for the understanding of these ...Chaperonins play an important role in folding newly synthesized or translocated proteins in all organisms. The bacterial chaperonin GroEL has served as a model system for the understanding of these proteins. In comparison, its human homolog, known as mitochondrial heat shock protein family member D1 (HSPD1) is poorly understood. Here, we present the structure of HSPD1 in the apo state determined by cryo-electron microscopy (cryo-EM). Unlike GroEL, HSPD1 forms mostly single ring assemblies in the absence of co-chaperonin (HSPE1). Comparison with GroEL shows a rotation and increased flexibility of the apical domain. Together with published structures of the HSPD1/HSPE1 co-chaperonin complex, this work gives insight into the structural changes that occur during the catalytic cycle. This new understanding of HSPD1 structure and its rearrangements upon complex formation may provide new insights for the development of HSPD1-targeting treatments against a diverse range of diseases including glioblastoma. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11189.map.gz | 13.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11189-v30.xml emd-11189.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11189_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_11189.png | 188.4 KB | ||
Masks | emd_11189_msk_1.map | 58.2 MB | Mask map | |
Others | emd_11189_additional_1.map.gz emd_11189_additional_2.map.gz emd_11189_additional_3.map.gz emd_11189_half_map_1.map.gz emd_11189_half_map_2.map.gz | 1.9 MB 44 MB 1.8 MB 44.6 MB 44.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11189 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11189 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11189.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened, final map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_11189_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: monomer conformation 1 from symmetry expansion
File | emd_11189_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | monomer conformation 1 from symmetry expansion | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: unsharpened map
File | emd_11189_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: monomer conformation 2 from symmetry expansion
File | emd_11189_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | monomer conformation 2 from symmetry expansion | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_11189_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_11189_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : human mitochondrial heat shock protein family member D1 (HSPD1)
Entire | Name: human mitochondrial heat shock protein family member D1 (HSPD1) |
---|---|
Components |
|
-Supramolecule #1: human mitochondrial heat shock protein family member D1 (HSPD1)
Supramolecule | Name: human mitochondrial heat shock protein family member D1 (HSPD1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: produced by heterologous expression, mature HSPD1, apo state |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.3 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER / Details: blot time 0.5 s or 4 s. |
Details | the inverted double ring represented a small fraction of particles (< 10 %) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Average exposure time: 1.5 sec. / Average electron dose: 75.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |