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Yorodumi- PDB-8p0v: Structure of the human Commander complex coiled coils, DENND10 an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p0v | |||||||||||||||
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Title | Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex | |||||||||||||||
Components |
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Keywords | UNKNOWN FUNCTION / Coiled-coil / DENND domain / alpha solenoid / calponin homology | |||||||||||||||
Function / homology | Function and homology information WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / cytoplasmic sequestering of NF-kappaB / endosome transport via multivesicular body sorting pathway / retromer complex / Golgi to plasma membrane transport / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / retrograde transport, endosome to Golgi / regulation of early endosome to late endosome transport ...WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / cytoplasmic sequestering of NF-kappaB / endosome transport via multivesicular body sorting pathway / retromer complex / Golgi to plasma membrane transport / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / retrograde transport, endosome to Golgi / regulation of early endosome to late endosome transport / cullin family protein binding / ficolin-1-rich granule membrane / intracellular copper ion homeostasis / negative regulation of canonical NF-kappaB signal transduction / guanyl-nucleotide exchange factor activity / intracellular protein transport / small GTPase binding / late endosome / protein transport / Neddylation / positive regulation of canonical NF-kappaB signal transduction / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / nucleoplasm / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||||||||
Authors | Kumpula, E.P. / Laulumaa, S. / Huiskonen, J.T. | |||||||||||||||
Funding support | Finland, 4items
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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. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. #2: Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p0v.cif.gz | 288.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p0v.ent.gz | 187.5 KB | Display | PDB format |
PDBx/mmJSON format | 8p0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p0v_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8p0v_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8p0v_validation.xml.gz | 62.7 KB | Display | |
Data in CIF | 8p0v_validation.cif.gz | 98.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/8p0v ftp://data.pdbj.org/pub/pdb/validation_reports/p0/8p0v | HTTPS FTP |
-Related structure data
Related structure data | 17339MC 8p0wC 8p0xC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 73319.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T FlpIn T-REx / References: UniProt: Q567U6 |
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#2: Protein | Mass: 70856.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T FlpIn T-REx / References: UniProt: O60826 |
#3: Protein | Mass: 40562.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T FlpIn T-REx / References: UniProt: Q8TCE6 |
#4: Protein | Mass: 20531.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T FlpIn T-REx / References: UniProt: Q9UBQ0 |
#5: Protein | Mass: 109700.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T FlpIn T-REx / References: UniProt: Q7Z3J2 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human Commander Complex coiled coil region, partial Retriever subcomplex Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.56 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 55769 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 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 7700000 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 194.71 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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