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- EMDB-17341: Structure of the human Commander complex Retriever Subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-17341
TitleStructure of the human Commander complex Retriever Subcomplex
Map data
Sample
  • Complex: Human Commander Complex
    • Protein or peptide: Coiled-coil domain-containing protein 93
    • Protein or peptide: Coiled-coil domain-containing protein 22
    • Protein or peptide: Vacuolar protein sorting-associated protein 29Vacuole
    • Protein or peptide: VPS35 endosomal protein-sorting factor-like
    • Protein or peptide: Vacuolar protein sorting-associated protein 26CVacuole
Keywordsalpha solenoid / arrestin fold / phosphoesterase fold / complex / UNKNOWN FUNCTION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsKumpula EP / Laulumaa S / Huiskonen JT
Funding support Finland, 4 items
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, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17341.png

Downloads & links

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Map

FileDownload / File: emd_17341.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 560 pix.
= 473.984 Å		0.85 Å/pix.
x 560 pix.
= 473.984 Å		0.85 Å/pix.
x 560 pix.
= 473.984 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.15444845 - 0.30110538
Average (Standard dev.)-0.00026439846 (±0.0059329807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 473.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17341_msk_1.map
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Half map: #2

Fileemd_17341_half_map_1.map
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Half map: #1

Fileemd_17341_half_map_2.map
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Sample components

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Entire : Human Commander Complex

EntireName: Human Commander Complex
Components
  • Complex: Human Commander Complex
    • Protein or peptide: Coiled-coil domain-containing protein 93
    • Protein or peptide: Coiled-coil domain-containing protein 22
    • Protein or peptide: Vacuolar protein sorting-associated protein 29Vacuole
    • Protein or peptide: VPS35 endosomal protein-sorting factor-like
    • Protein or peptide: Vacuolar protein sorting-associated protein 26CVacuole

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Supramolecule #1: Human Commander Complex

SupramoleculeName: Human Commander Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 560 KDa

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

MacromoleculeName: Coiled-coil domain-containing protein 93 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.319734 KDa
SequenceString: MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEK IVSVLPRMKC PHQLEPHQIQ GMDFIHIFPV VQWLVKRAIE TKEEMGDYIR SYSVSQFQKT YSLPEDDDFI K RKEKAIKT ...String:
MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEK IVSVLPRMKC PHQLEPHQIQ GMDFIHIFPV VQWLVKRAIE TKEEMGDYIR SYSVSQFQKT YSLPEDDDFI K RKEKAIKT VVDLSEVYKP RRKYKRHQGA EELLDEESRI HATLLEYGRR YGFSRQSKME KAEDKKTALP AGLSATEKAD AH EEDELRA AEEQRIQSLM TKMTAMANEE SRLTASSVGQ IVGLCSAEIK QIVSEYAEKQ SELSAEESPE KLGTSQLHRR KVI SLNKQI AQKTKHLEEL RASHTSLQAR YNEAKKTLTE LKTYSEKLDK EQAALEKIES KADPSILQNL RALVAMNENL KSQE QEFKA HCREEMTRLQ QEIENLKAER APRGDEKTLS SGEPPGTLTS AMTHDEDLDR RYNMEKEKLY KIRLLQARRN REIAI LHRK IDEVPSRAEL IQYQKRFIEL YRQISAVHKE TKQFFTLYNT LDDKKVYLEK EISLLNSIHE NFSQAMASPA ARDQFL RQM EQIVEGIKQS RMKMEKKKQE NKMRRDQLND QYLELLEKQR LYFKTVKEFK EEGRKNEMLL SKVKAKAS

UniProtKB: Coiled-coil domain-containing protein 93

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

MacromoleculeName: Coiled-coil domain-containing protein 22 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.856555 KDa
SequenceString: MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNF LYPSEPDLRD LLLFLAERLP TDASEDADQP AGDSAILLRA IGSQIRDQLA LPWVPPHLRT PKLQHLQGSA L QKPFHASR ...String:
MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNF LYPSEPDLRD LLLFLAERLP TDASEDADQP AGDSAILLRA IGSQIRDQLA LPWVPPHLRT PKLQHLQGSA L QKPFHASR LVVPELSSRG EPREFQASPL LLPVPTQVPQ PVGRVASLLE HHALQLCQQT GRDRPGDEDW VHRTSRLPPQ ED TRAQRQR LQKQLTEHLR QSWGLLGAPI QARDLGELLQ AWGAGAKTGA PKGSRFTHSE KFTFHLEPQA QATQVSDVPA TSR RPEQVT WAAQEQELES LREQLEGVNR SIEEVEADMK TLGVSFVQAE SECRHSKLST AEREQALRLK SRAVELLPDG TANL AKLQL VVENSAQRVI HLAGQWEKHR VPLLAEYRHL RKLQDCRELE SSRRLAEIQE LHQSVRAAAE EARRKEEVYK QLMSE LETL PRDVSRLAYT QRILEIVGNI RKQKEEITKI LSDTKELQKE INSLSGKLDR TFAVTDELVF KDAKKDDAVR KAYKYL AAL HENCSQLIQT IEDTGTIMRE VRDLEEQIET ELGKKTLSNL EKIREDYRAL RQENAGLLGR VREA

UniProtKB: Coiled-coil domain-containing protein 22

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Macromolecule #3: Vacuolar protein sorting-associated protein 29

MacromoleculeName: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.531705 KDa
SequenceString:
MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQ VIPWGDMASL ALLQRQFDVD ILISGHTHKF EAFEHENKFY INPGSATGAY NALETNIIPS FVLMDIQAST V VTYVYQLI GDDVKVERIE YKKP

UniProtKB: Vacuolar protein sorting-associated protein 29

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Macromolecule #4: VPS35 endosomal protein-sorting factor-like

MacromoleculeName: VPS35 endosomal protein-sorting factor-like / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.700453 KDa
SequenceString: MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPA ALAAAMDSSR RKRDRDDNSV VGSDFEPWTN KRGEILARYT TTEKLSINLF MGSEKGKAGT ATLAMSEKVR T RLEELDDF ...String:
MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPA ALAAAMDSSR RKRDRDDNSV VGSDFEPWTN KRGEILARYT TTEKLSINLF MGSEKGKAGT ATLAMSEKVR T RLEELDDF EEGSQKELLN LTQQDYVNRI EELNQSLKDA WASDQKVKAL KIVIQCSKLL SDTSVIQFYP SKFVLITDIL DT FGKLVYE RIFSMCVDSR SVLPDHFSPE NANDTAKETC LNWFFKIASI RELIPRFYVE ASILKCNKFL SKTGISECLP RLT CMIRGI GDPLVSVYAR AYLCRVGMEV APHLKETLNK NFFDFLLTFK QIHGDTVQNQ LVVQGVELPS YLPLYPPAMD WIFQ CISYH APEALLTEMM ERCKKLGNNA LLLNSVMSAF RAEFIATRSM DFIGMIKECD ESGFPKHLLF RSLGLNLALA DPPES DRLQ ILNEAWKVIT KLKNPQDYIN CAEVWVEYTC KHFTKREVNT VLADVIKHMT PDRAFEDSYP QLQLIIKKVI AHFHDF SVL FSVEKFLPFL DMFQKESVRV EVCKCIMDAF IKHQQEPTKD PVILNALLHV CKTMHDSVNA LTLEDEKRML SYLINGF IK MVSFGRDFEQ QLSFYVESRS MFCNLEPVLV QLIHSVNRLA METRKVMKGN HSRKTAAFVR ACVAYCFITI PSLAGIFT R LNLYLHSGQV ALANQCLSQA DAFFKAAISL VPEVPKMINI DGKMRPSESF LLEFLCNFFS TLLIVPDHPE HGVLFLVRE LLNVIQDYTW EDNSDEKIRI YTCVLHLLSA MSQETYLYHI DKVDSNDSLY GGDSKFLAEN NKLCETVMAQ ILEHLKTLAK DEALKRQSS LGLSFFNSIL AHGDLRNNKL NQLSVNLWHL AQRHGCADTR TMVKTLEYIK KQSKQPDMTH LTELALRLPL Q TRT

UniProtKB: VPS35 endosomal protein-sorting factor-like

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Macromolecule #5: Vacuolar protein sorting-associated protein 26C

MacromoleculeName: Vacuolar protein sorting-associated protein 26C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.049344 KDa
SequenceString: MGTALDIKIK RANKVYHAGE VLSGVVVISS KDSVQHQGVS LTMEGTVNLQ LSAKSVGVFE AFYNSVKPIQ IINSTIEMVK PGKFPSGKT EIPFEFPLHL KGNKVLYETY HGVFVNIQYT LRCDMKRSLL AKDLTKTCEF IVHSAPQKGK FTPSPVDFTI T PETLQNVK ...String:
MGTALDIKIK RANKVYHAGE VLSGVVVISS KDSVQHQGVS LTMEGTVNLQ LSAKSVGVFE AFYNSVKPIQ IINSTIEMVK PGKFPSGKT EIPFEFPLHL KGNKVLYETY HGVFVNIQYT LRCDMKRSLL AKDLTKTCEF IVHSAPQKGK FTPSPVDFTI T PETLQNVK ERALLPKFLL RGHLNSTNCV ITQPLTGELV VESSEAAIRS VELQLVRVET CGCAEGYARD ATEIQNIQIA DG DVCRGLS VPIYMVFPRL FTCPTLETTN FKVEFEVNIV VLLHPDHLIT ENFPLKLCRI

UniProtKB: Vacuolar protein sorting-associated protein 26C

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.107 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 55769 / Average electron dose: 59.0 e/Å2
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7700000
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 13000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8p0x:
Structure of the human Commander complex Retriever Subcomplex

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