[English] 日本語
Yorodumi
- PDB-8p0w: Structure of the human Commander complex COMMD ring -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p0w
TitleStructure of the human Commander complex COMMD ring
Components
  • (COMM domain-containing protein ...) x 10
  • (Coiled-coil domain-containing protein ...) x 2
KeywordsUNKNOWN FUNCTION / COMMD fold / calponin homology fold / pseudo-C5 symmetry
Function / homology
Function and homology information


negative regulation of sodium ion transmembrane transport / cytoplasmic sequestering of NF-kappaB / plasma membrane to endosome transport / 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 / sodium channel inhibitor activity / positive regulation of ubiquitin-dependent protein catabolic process ...negative regulation of sodium ion transmembrane transport / cytoplasmic sequestering of NF-kappaB / plasma membrane to endosome transport / 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 / sodium channel inhibitor activity / positive regulation of ubiquitin-dependent protein catabolic process / phosphatidylinositol-3,4-bisphosphate binding / endocytic recycling / phosphatidylinositol-3,5-bisphosphate binding / Cul2-RING ubiquitin ligase complex / negative regulation of NF-kappaB transcription factor activity / sodium ion transport / phosphatidylinositol-3,4,5-trisphosphate binding / cullin family protein binding / NF-kappaB binding / intracellular copper ion homeostasis / negative regulation of canonical NF-kappaB signal transduction / phosphatidylinositol-4,5-bisphosphate binding / tumor necrosis factor-mediated signaling pathway / cholesterol homeostasis / positive regulation of protein ubiquitination / nucleotide-excision repair / recycling endosome / protein transport / Neddylation / cytoplasmic vesicle / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / early endosome / endosome membrane / 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 / cytosol / cytoplasm
Similarity search - Function
COMM domain-containing protein 2 / COMM domain-containing protein 3 / COMM domain-containing protein 4 / : / COMMD8, helical N-terminal domain / COMMD1 N-terminal domain / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 7 / COMM domain-containing protein 10 ...COMM domain-containing protein 2 / COMM domain-containing protein 3 / COMM domain-containing protein 4 / : / COMMD8, helical N-terminal domain / COMMD1 N-terminal domain / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 7 / COMM domain-containing protein 10 / : / COMMD1 N-terminal domain / COMMD2-7/10, HN 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 / COMM domain-containing protein 9 / : / COMMD9, helical N-terminal domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
Coiled-coil domain-containing protein 22 / Coiled-coil domain-containing protein 93 / COMM domain-containing protein 6 / COMM domain-containing protein 7 / COMM domain-containing protein 2 / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 4 / COMM domain-containing protein 8 / COMM domain-containing protein 9 ...Coiled-coil domain-containing protein 22 / Coiled-coil domain-containing protein 93 / COMM domain-containing protein 6 / COMM domain-containing protein 7 / COMM domain-containing protein 2 / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 4 / COMM domain-containing protein 8 / COMM domain-containing protein 9 / COMM domain-containing protein 3 / COMM domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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
Revision 1.1Jul 3, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COMM domain-containing protein 1
B: COMM domain-containing protein 2
C: COMM domain-containing protein 3
D: COMM domain-containing protein 4
E: COMM domain-containing protein 5
F: COMM domain-containing protein 6
G: COMM domain-containing protein 7
H: COMM domain-containing protein 8
I: COMM domain-containing protein 9
J: COMM domain-containing protein 10
K: Coiled-coil domain-containing protein 93
L: Coiled-coil domain-containing protein 22


Theoretical massNumber of molelcules
Total (without water)354,99012
Polymers354,99012
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area61030 Å2
ΔGint-378 kcal/mol
Surface area101260 Å2
MethodPISA

-
Components

-
COMM domain-containing protein ... , 10 types, 10 molecules ABCDEFGHIJ

#1: Protein COMM domain-containing protein 1 / Protein Murr1


Mass: 21203.061 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: Q8N668
#2: Protein COMM domain-containing protein 2


Mass: 22776.113 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: Q86X83
#3: Protein COMM domain-containing protein 3 / Protein Bup / Protein PIL


Mass: 22179.117 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: Q9UBI1
#4: Protein COMM domain-containing protein 4


Mass: 21790.354 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: Q9H0A8
#5: Protein COMM domain-containing protein 5 / Hypertension-related calcium-regulated gene protein / HCaRG


Mass: 24699.361 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: Q9GZQ3
#6: Protein COMM domain-containing protein 6


Mass: 9648.074 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: Q7Z4G1
#7: Protein COMM domain-containing protein 7


Mass: 22561.953 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: Q86VX2
#8: Protein COMM domain-containing protein 8


Mass: 21116.342 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: Q9NX08
#9: Protein COMM domain-containing protein 9


Mass: 21844.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bait for capturing the endogenous complex / Source: (natural) Homo sapiens (human) / Cell line: HEK293T FlpIn T-REx / References: UniProt: Q9P000
#10: Protein COMM domain-containing protein 10


Mass: 22995.402 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: Q9Y6G5

-
Coiled-coil domain-containing protein ... , 2 types, 2 molecules KL

#11: 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
#12: 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

-
Non-polymers , 1 types, 21 molecules

#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
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: #1-#12 / 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 FIELD / 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
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
1cryoSPARC4.1.1particle selection
4cryoSPARC4.1.1CTF correction
7ISOLDE1.5model fitting
9cryoSPARC4.1.1initial Euler assignment
10cryoSPARC4.1.1final Euler assignment
11cryoSPARC4.1.1classification
12cryoSPARC4.1.13D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7700000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 667000 / 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: 32.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003717789
ELECTRON MICROSCOPYf_angle_d0.644224028
ELECTRON MICROSCOPYf_chiral_restr0.04292767
ELECTRON MICROSCOPYf_plane_restr0.01073085
ELECTRON MICROSCOPYf_dihedral_angle_d13.23416746

+
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