[English] 日本語
Yorodumi
- PDB-8p0x: Structure of the human Commander complex Retriever Subcomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p0x
TitleStructure of the human Commander complex Retriever Subcomplex
Components
  • Coiled-coil domain-containing protein 22
  • Coiled-coil domain-containing protein 93
  • VPS35 endosomal protein-sorting factor-like
  • Vacuolar protein sorting-associated protein 26CVacuole
  • Vacuolar protein sorting-associated protein 29Vacuole
KeywordsUNKNOWN FUNCTION / alpha solenoid / arrestin fold / phosphoesterase fold / complex
Function / homology
Function and homology information


retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / cytoplasmic sequestering of NF-kappaB / retromer complex / Golgi to plasma membrane transport / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / retrograde transport, endosome to Golgi / cullin family protein binding / ficolin-1-rich granule membrane ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / cytoplasmic sequestering of NF-kappaB / retromer complex / Golgi to plasma membrane transport / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / retrograde transport, endosome to Golgi / cullin family protein binding / ficolin-1-rich granule membrane / intracellular copper ion homeostasis / negative regulation of canonical NF-kappaB signal transduction / intracellular protein transport / 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 / nucleus / plasma membrane / cytosol
Similarity search - Function
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 ...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 protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Arrestin-like, C-terminal / Metallo-dependent phosphatase-like / Immunoglobulin E-set
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 26C / Coiled-coil domain-containing protein 22 / Coiled-coil domain-containing protein 93 / VPS35 endosomal protein-sorting factor-like / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 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
CitationJournal: 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
DepositionMay 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
K: Coiled-coil domain-containing protein 93
L: Coiled-coil domain-containing protein 22
N: Vacuolar protein sorting-associated protein 29
O: VPS35 endosomal protein-sorting factor-like
P: Vacuolar protein sorting-associated protein 26C


Theoretical massNumber of molelcules
Total (without water)307,4585
Polymers307,4585
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5520 Å2
ΔGint-67 kcal/mol
Surface area104950 Å2
MethodPISA

-
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 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
#4: 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
#5: Protein Vacuolar protein sorting-associated protein 26C / Vacuole / Down syndrome critical region protein 3 / Down syndrome critical region protein A


Mass: 33049.344 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: O14972

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Human Commander Complex / 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

-
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

-
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
9PHENIX1.2model refinement
10cryoSPARC4.1.1initial Euler assignment
11cryoSPARC4.1.1final Euler assignment
12cryoSPARC4.1.1classification
13cryoSPARC4.1.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7700000
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more