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- PDB-8f2u: Human CCC complex -

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Basic information

Entry
Database: PDB / ID: 8f2u
TitleHuman CCC complex
Components
  • (COMM domain-containing protein ...) x 10
  • (Coiled-coil domain-containing protein ...) x 2
KeywordsENDOCYTOSIS / endosomal sorting / commander / CCC complex
Function / homology
Function and homology information


positive regulation of cholesterol import / positive regulation of endosome to plasma membrane protein transport / negative regulation of sodium ion transmembrane transport / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / plasma membrane to endosome transport / low-density lipoprotein particle clearance / copper ion homeostasis / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / Golgi to plasma membrane transport ...positive regulation of cholesterol import / positive regulation of endosome to plasma membrane protein transport / negative regulation of sodium ion transmembrane transport / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / plasma membrane to endosome transport / low-density lipoprotein particle clearance / copper ion homeostasis / regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein localization to cell surface / Golgi to plasma membrane transport / phosphatidic acid binding / endocytic recycling / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of protein localization to cell surface / sodium channel inhibitor activity / positive regulation of ubiquitin-dependent protein catabolic process / phosphatidylinositol-3,5-bisphosphate binding / protein localization to cell surface / 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 / intracellular copper ion homeostasis / NF-kappaB binding / phosphatidylinositol-4,5-bisphosphate binding / negative regulation of canonical NF-kappaB signal transduction / cholesterol homeostasis / positive regulation of protein ubiquitination / tumor necrosis factor-mediated signaling pathway / nucleotide-excision repair / recycling endosome / protein destabilization / protein transport / Neddylation / cytoplasmic vesicle / secretory granule lumen / ficolin-1-rich granule lumen / early endosome / positive regulation of canonical NF-kappaB signal transduction / endosome / endosome membrane / copper ion binding / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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 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: 3.53 Å
AuthorsHealy, M.D. / McNally, K.E. / Butkovic, R. / Chilton, M. / Kato, K. / Sacharz, J. / McConville, C. / Moody, E.R.R. / Shaw, S. / Planelles-Herrero, V.J. ...Healy, M.D. / McNally, K.E. / Butkovic, R. / Chilton, M. / Kato, K. / Sacharz, J. / McConville, C. / Moody, E.R.R. / Shaw, S. / Planelles-Herrero, V.J. / Kadapalakere, S.Y. / Ross, J. / Borucu, U. / Palmer, C.S. / Chen, K. / Croll, T.I. / Hall, R.J. / Caruana, N.J. / Ghai, R. / Nguyen, T.H.D. / Heesom, K.J. / Saitoh, S. / Berger, I. / Berger-Schaffitzel, C. / Williams, T.A. / Stroud, D.A. / Derivery, E. / Collins, B.M. / Cullen, P.J.
Funding support United Kingdom, Australia, 9items
OrganizationGrant numberCountry
Wellcome Trust104568/Z/14/Z United Kingdom
Wellcome Trust220260/Z/20/Z United Kingdom
Wellcome Trust220480/Z/20/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L007363/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/P018807/1 United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
Royal SocietyRSRP/R1/211004 United Kingdom
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1156493 Australia
CitationJournal: Cell / Year: 2023
Title: Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome.
Authors: Michael D Healy / Kerrie E McNally / Rebeka Butkovič / Molly Chilton / Kohji Kato / Joanna Sacharz / Calum McConville / Edmund R R Moody / Shrestha Shaw / Vicente J Planelles-Herrero / ...Authors: Michael D Healy / Kerrie E McNally / Rebeka Butkovič / Molly Chilton / Kohji Kato / Joanna Sacharz / Calum McConville / Edmund R R Moody / Shrestha Shaw / Vicente J Planelles-Herrero / Sathish K N Yadav / Jennifer Ross / Ufuk Borucu / Catherine S Palmer / Kai-En Chen / Tristan I Croll / Ryan J Hall / Nikeisha J Caruana / Rajesh Ghai / Thi H D Nguyen / Kate J Heesom / Shinji Saitoh / Imre Berger / Christiane Schaffitzel / Tom A Williams / David A Stroud / Emmanuel Derivery / Brett M Collins / Peter J Cullen /
Abstract: The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, ...The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.
History
DepositionNov 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
N: Coiled-coil domain-containing protein 93
T: Coiled-coil domain-containing protein 22


Theoretical massNumber of molelcules
Total (without water)360,01912
Polymers360,01912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, immunoprecipitation, native gel electrophoresis, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD1, C2orf5, MURR1 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q8N668
#2: Protein COMM domain-containing protein 2


Mass: 22776.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD2, HSPC042, My004 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD3, BUP, C10orf8 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q9UBI1
#4: Protein COMM domain-containing protein 4


Mass: 21790.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD4 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q9H0A8
#5: Protein COMM domain-containing protein 5 / Hypertension-related calcium-regulated gene protein / HCaRG


Mass: 28346.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD5, HT002 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q9GZQ3
#6: Protein COMM domain-containing protein 6


Mass: 9648.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD6, MSTP076 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q7Z4G1
#7: Protein COMM domain-containing protein 7


Mass: 22561.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD7, C20orf92 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q86VX2
#8: Protein COMM domain-containing protein 8


Mass: 21116.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD8, MDS022 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q9NX08
#9: Protein COMM domain-containing protein 9


Mass: 21844.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD9, HSPC166 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q9P000
#10: Protein COMM domain-containing protein 10


Mass: 24376.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD10, HSPC305, PTD002 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q9Y6G5

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

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


Mass: 73319.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC93 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: Q567U6
#12: Protein Coiled-coil domain-containing protein 22


Mass: 70856.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC22, CXorf37, JM1 / Cell line (production host): Sf21 / Production host: Spodoptera (butterflies/moths) / References: UniProt: O60826

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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 CCC complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera (butterflies/moths) / Strain: Sf21
Buffer solutionpH: 7.2
Details: 50 mM HEPES pH7.2, 150 mM NaCl, 2mM beta-mercaptoethanol, 0.01% Triton-X100
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Human CCC complex cross-linked with 1 mM BS3
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingAverage exposure time: 9.01 sec. / Electron dose: 43.14 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5651

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4CTFFIND4CTF correction
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20034 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002119383
ELECTRON MICROSCOPYf_angle_d0.476226191
ELECTRON MICROSCOPYf_chiral_restr0.05523012
ELECTRON MICROSCOPYf_plane_restr0.00353372
ELECTRON MICROSCOPYf_dihedral_angle_d3.80972575

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