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- PDB-8p0v: Structure of the human Commander complex coiled coils, DENND10 an... -

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Basic information

Entry
Database: PDB / ID: 8p0v
TitleStructure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex
Components
  • Coiled-coil domain-containing protein 22
  • Coiled-coil domain-containing protein 93
  • DENN domain-containing protein 10
  • VPS35 endosomal protein-sorting factor-like
  • Vacuolar protein sorting-associated protein 29Vacuole
KeywordsUNKNOWN FUNCTION / Coiled-coil / DENND domain / alpha solenoid / calponin homology
Function / homology
Function and homology information


retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / 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 ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / 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 / protein transport / late endosome / 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
DENN domain-containing protein 10 / Stabilization of polarity axis / Tripartite DENN domain / Tripartite DENN domain profile. / Coiled-coil domain-containing protein 22 / CCDC93, coiled-coil domain / Coiled-coil domain-containing protein 93 / : / : / : ...DENN domain-containing protein 10 / Stabilization of polarity axis / Tripartite DENN domain / Tripartite DENN domain profile. / Coiled-coil domain-containing protein 22 / CCDC93, coiled-coil domain / Coiled-coil domain-containing protein 93 / : / : / : / CCDC22 protein coiled-coil region / CCDC93 coiled-coil domain / CCDC93 protein N-terminal domain / CCDC22 protein N-terminal domain / VPS35 endosomal protein sorting factor-like / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Coiled-coil domain-containing protein 22 / Coiled-coil domain-containing protein 93 / VPS35 endosomal protein-sorting factor-like / DENN domain-containing protein 10 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsKumpula, E.P. / Laulumaa, S. / Huiskonen, J.T.
Funding support Finland, 4items
OrganizationGrant numberCountry
Academy of Finland288475 Finland
Academy of Finland319303 Finland
Academy of Finland336470 Finland
Academy of Finland314669 Finland
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
DepositionMay 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Coiled-coil domain-containing protein 93
L: Coiled-coil domain-containing protein 22
M: DENN domain-containing protein 10
N: Vacuolar protein sorting-associated protein 29
O: VPS35 endosomal protein-sorting factor-like


Theoretical massNumber of molelcules
Total (without water)314,9715
Polymers314,9715
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8840 Å2
ΔGint-116 kcal/mol
Surface area99110 Å2
MethodPISA

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Components

#1: Protein Coiled-coil domain-containing protein 93


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
#2: Protein Coiled-coil domain-containing protein 22


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 DENN domain-containing protein 10 / Protein FAM45A


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 Vacuolar protein sorting-associated protein 29 / Vacuole / hVPS29 / PEP11 homolog / Vesicle protein sorting 29


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 VPS35 endosomal protein-sorting factor-like / Esophageal cancer-associated 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human Commander Complex coiled coil region, partial Retriever subcomplex
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.56 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
UCSF ChimeraX1.5/v9model building
EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
4cryoSPARC4.1.1CTF correction
7ISOLDE1.5model fitting
9cryoSPARC4.1.1initial Euler assignment
10cryoSPARC4.1.1final Euler assignment
12cryoSPARC4.1.13D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7700000
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 194.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010314836
ELECTRON MICROSCOPYf_angle_d1.336920008
ELECTRON MICROSCOPYf_chiral_restr0.06552271
ELECTRON MICROSCOPYf_plane_restr0.01252563
ELECTRON MICROSCOPYf_dihedral_angle_d16.68765679

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