+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17340 | |||||||||||||||
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Title | Structure of the human Commander complex COMMD ring | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | COMMD fold / calponin homology fold / pseudo-C5 symmetry / UNKNOWN FUNCTION | |||||||||||||||
Function / homology | Function and homology information negative regulation of sodium ion transmembrane transport / plasma membrane to endosome transport / cytoplasmic sequestering of NF-kappaB / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / copper ion homeostasis / Golgi to plasma membrane transport / phosphatidic acid binding / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling ...negative regulation of sodium ion transmembrane transport / plasma membrane to endosome transport / cytoplasmic sequestering of NF-kappaB / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / copper ion homeostasis / Golgi to plasma membrane transport / phosphatidic acid binding / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / phosphatidylinositol-3,4-bisphosphate binding / sodium channel inhibitor activity / phosphatidylinositol-3,5-bisphosphate binding / Cul2-RING ubiquitin ligase complex / negative regulation of NF-kappaB transcription factor activity / sodium ion transport / cullin family protein binding / phosphatidylinositol-3,4,5-trisphosphate binding / NF-kappaB binding / intracellular copper ion homeostasis / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of protein ubiquitination / cholesterol homeostasis / nucleotide-excision repair / recycling endosome / protein transport / Neddylation / positive regulation of canonical NF-kappaB signal transduction / cytoplasmic vesicle / secretory granule lumen / ficolin-1-rich granule lumen / endosome / endosome membrane / early endosome / copper ion binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Kumpula EP / Laulumaa S / Huiskonen JT | |||||||||||||||
Funding support | Finland, 4 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structure and interactions of the endogenous human Commander complex. Authors: Saara Laulumaa / Esa-Pekka Kumpula / Juha T Huiskonen / Markku Varjosalo / Abstract: The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil ...The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil domain-containing proteins (CCDC22 and CCDC93), DENND10 and the Retriever subcomplex (VPS26C, VPS29 and VPS35L), all expressed ubiquitously in the body and linked to various diseases. Here, we report the structure and key interactions of the endogenous human Commander complex by cryogenic-electron microscopy and mass spectrometry-based proteomics. The complex consists of a stable core of COMMD1-10 and an effector containing DENND10 and Retriever, scaffolded together by CCDC22 and CCDC93. We establish the composition of Commander and reveal major interaction interfaces. These findings clarify its roles in intracellular transport, and uncover a strong association with cilium assembly, and centrosome and centriole functions. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17340.map.gz | 633.1 MB | EMDB map data format | |
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Header (meta data) | emd-17340-v30.xml emd-17340.xml | 29.4 KB 29.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17340_fsc.xml | 18.6 KB | Display | FSC data file |
Images | emd_17340.png | 154.4 KB | ||
Masks | emd_17340_msk_1.map | 669.9 MB | Mask map | |
Filedesc metadata | emd-17340.cif.gz | 8.3 KB | ||
Others | emd_17340_half_map_1.map.gz emd_17340_half_map_2.map.gz | 620.7 MB 620.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17340 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17340 | HTTPS FTP |
-Validation report
Summary document | emd_17340_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17340_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17340_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | emd_17340_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17340 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17340 | HTTPS FTP |
-Related structure data
Related structure data | 8p0wMC 8p0vC 8p0xC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17340.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17340_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17340_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17340_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human Commander Complex
+Supramolecule #1: Human Commander Complex
+Macromolecule #1: COMM domain-containing protein 1
+Macromolecule #2: COMM domain-containing protein 2
+Macromolecule #3: COMM domain-containing protein 3
+Macromolecule #4: COMM domain-containing protein 4
+Macromolecule #5: COMM domain-containing protein 5
+Macromolecule #6: COMM domain-containing protein 6
+Macromolecule #7: COMM domain-containing protein 7
+Macromolecule #8: COMM domain-containing protein 8
+Macromolecule #9: COMM domain-containing protein 9
+Macromolecule #10: COMM domain-containing protein 10
+Macromolecule #11: Coiled-coil domain-containing protein 93
+Macromolecule #12: Coiled-coil domain-containing protein 22
+Macromolecule #13: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec. / Pretreatment - Pressure: 0.107 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 55769 / Average electron dose: 59.0 e/Å2 Details: Two datasets were collected from identical grids prepared in the same session. Dataset 1: 20675 movies 50 frames / movie 59 e-/A2 total dose Dataset 2: 35084 movies 45 frames / movie 56 e-/A2 total dose |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-8p0w: |