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- EMDB-17342: Human Commander complex (native) -

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Basic information

Entry
Database: EMDB / ID: EMD-17342
TitleHuman Commander complex (native)
Map data
Sample
  • Complex: Human Commander Complex
    • Protein or peptide: x 16 types
KeywordsCOMMD fold / calponin homology fold / pseudo-C5 symmetry / UNKNOWN FUNCTION
Function / homology
Function and homology information


negative regulation of sodium ion transmembrane transport / retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / plasma membrane to endosome transport / cytoplasmic sequestering of NF-kappaB / regulation of proteasomal ubiquitin-dependent protein catabolic process / endosome transport via multivesicular body sorting pathway / retromer complex / copper ion homeostasis / negative regulation of protein localization to cell surface ...negative regulation of sodium ion transmembrane transport / retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / plasma membrane to endosome transport / cytoplasmic sequestering of NF-kappaB / regulation of proteasomal ubiquitin-dependent protein catabolic process / endosome transport via multivesicular body sorting pathway / retromer complex / copper ion homeostasis / negative regulation of protein localization to cell surface / Golgi to plasma membrane transport / phosphatidic acid binding / positive regulation of ubiquitin-dependent protein catabolic process / endocytic recycling / phosphatidylinositol-3,4-bisphosphate binding / sodium channel inhibitor activity / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / Cul2-RING ubiquitin ligase complex / regulation of early endosome to late endosome transport / sodium ion transport / negative regulation of NF-kappaB transcription factor activity / cullin family protein binding / phosphatidylinositol-3,4,5-trisphosphate binding / ficolin-1-rich granule membrane / intracellular copper ion homeostasis / NF-kappaB binding / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / cholesterol homeostasis / positive regulation of protein ubiquitination / nucleotide-excision repair / intracellular protein transport / recycling endosome / small GTPase binding / protein transport / late endosome / Neddylation / cytoplasmic vesicle / positive regulation of canonical NF-kappaB signal transduction / secretory granule lumen / ficolin-1-rich granule lumen / early endosome / endosome membrane / endosome / copper ion binding / intracellular membrane-bounded organelle / centrosome / negative regulation of DNA-templated transcription / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular region / nucleoplasm / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DENN domain-containing protein 10 / Stabilization of polarity axis / COMM domain-containing protein 2 / COMM domain-containing protein 3 / COMM domain-containing protein 4 / : / COMMD1 N-terminal domain / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 7 ...DENN domain-containing protein 10 / Stabilization of polarity axis / COMM domain-containing protein 2 / COMM domain-containing protein 3 / COMM domain-containing protein 4 / : / COMMD1 N-terminal domain / COMM domain-containing protein 1 / COMM domain-containing protein 5 / COMM domain-containing protein 7 / COMM domain-containing protein 10 / Tripartite DENN domain / : / COMMD1 N-terminal domain / COMMD protein HN 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 / COMM domain-containing protein 9 / : / COMMD9, N-terminal domain / COMM domain / VPS35 endosomal protein sorting factor-like / COMM domain / COMM domain profile. / 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 / COMM domain-containing protein 6 / COMM domain-containing protein 7 / COMM domain-containing protein 2 / COMM domain-containing protein 1 / DENN domain-containing protein 10 / COMM domain-containing protein 5 ...Vacuolar protein sorting-associated protein 26C / Coiled-coil domain-containing protein 22 / Coiled-coil domain-containing protein 93 / VPS35 endosomal protein-sorting factor-like / COMM domain-containing protein 6 / COMM domain-containing protein 7 / COMM domain-containing protein 2 / COMM domain-containing protein 1 / DENN domain-containing protein 10 / 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 / Vacuolar protein sorting-associated protein 29 / COMM domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKumpula EP / 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_17342.png

Downloads & links

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Map

FileDownload / File: emd_17342.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 576 pix.
= 483.84 Å		0.84 Å/pix.
x 576 pix.
= 483.84 Å		0.84 Å/pix.
x 576 pix.
= 483.84 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.5365492 - 2.2980993
Average (Standard dev.)-0.000019719986 (±0.032250665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 483.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17342_msk_1.map
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Half map: #1

Fileemd_17342_half_map_1.map
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Half map: #2

Fileemd_17342_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: COMMD1
    • Protein or peptide: COMMD2
    • Protein or peptide: COMMD3
    • Protein or peptide: COMMD4
    • Protein or peptide: COMMD5
    • Protein or peptide: COMMD6
    • Protein or peptide: COMMD7
    • Protein or peptide: COMMD8
    • Protein or peptide: COMMD9
    • Protein or peptide: COMMD10
    • Protein or peptide: CCDC93
    • Protein or peptide: CCDC22
    • Protein or peptide: VPS29
    • Protein or peptide: VPS35L
    • Protein or peptide: VPS26C
    • Protein or peptide: DENND10

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Supramolecule #1: Human Commander Complex

SupramoleculeName: Human Commander Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Sample contains all components of the complex. However, only COMMD1-10, and parts of CCDC93 and CCDC22 are visible in this map.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 560 KDa

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Macromolecule #1: COMMD1

MacromoleculeName: COMMD1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MAAGELEGGK PLSGLLNALA QDTFHGYPGI TEELLRSQLY PEVPPEEFRP FLAKMRGILK SIASADMDFN QLEAFLTAQT KKQGGITSDQ AAVISKFWKS HKTKIRESLM NQSRWNSGLR GLSWRVDGKS QSRHSAQIHT PVAIIELELG KYGQESEFLC LEFDEVKVNQ ILKTLSEVEE SISTLISQPN

UniProtKB: COMM domain-containing protein 1

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Macromolecule #2: COMMD2

MacromoleculeName: COMMD2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MLLELSEEHK EHLAFLPQVD SAVVAEFGRI AVEFLRRGAN PKIYEGAARK LNVSSDTVQH GVEGLTYLLT ESSKLMISEL DFQDSVFVLG FSEELNKLLL QLYLDNRKEI RTILSELAPS LPSYHNLEWR LDVQLASRSL RQQIKPAVTI KLHLNQNGDH NTKVLQTDPA ...String:
MLLELSEEHK EHLAFLPQVD SAVVAEFGRI AVEFLRRGAN PKIYEGAARK LNVSSDTVQH GVEGLTYLLT ESSKLMISEL DFQDSVFVLG FSEELNKLLL QLYLDNRKEI RTILSELAPS LPSYHNLEWR LDVQLASRSL RQQIKPAVTI KLHLNQNGDH NTKVLQTDPA TLLHLVQQLE QALEEMKTNH CRRVVRNIK

UniProtKB: COMM domain-containing protein 2

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Macromolecule #3: COMMD3

MacromoleculeName: COMMD3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MELSESVQKG FQMLADPRSF DSNAFTLLLR AAFQSLLDAQ ADEAVLDHPD LKHIDPVVLK HCHAAAATYI LEAGKHRADK STLSTYLEDC KFDRERIELF CTEYQNNKNS LEILLGSIGR SLPHITDVSW RLEYQIKTNQ LHRMYRPAYL VTLSVQNTDS PSYPEISFSC ...String:
MELSESVQKG FQMLADPRSF DSNAFTLLLR AAFQSLLDAQ ADEAVLDHPD LKHIDPVVLK HCHAAAATYI LEAGKHRADK STLSTYLEDC KFDRERIELF CTEYQNNKNS LEILLGSIGR SLPHITDVSW RLEYQIKTNQ LHRMYRPAYL VTLSVQNTDS PSYPEISFSC SMEQLQDLVG KLKDASKSLE RATQL

UniProtKB: COMM domain-containing protein 3

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Macromolecule #4: COMMD4

MacromoleculeName: COMMD4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MRFRFCGDLD CPDWVLAEIS TLAKMSSVKL RLLCSQVLKE LLGQGIDYEK ILKLTADAKF ESGDVKATVA VLSFILSSAA KHSVDGESLS SELQQLGLPK EHAASLCRCY EEKQSPLQKH LRVCSLRMNR LAGVGWRVDY TLSSSLLQSV EEPMVHLRLE VAAAPGTPAQ ...String:
MRFRFCGDLD CPDWVLAEIS TLAKMSSVKL RLLCSQVLKE LLGQGIDYEK ILKLTADAKF ESGDVKATVA VLSFILSSAA KHSVDGESLS SELQQLGLPK EHAASLCRCY EEKQSPLQKH LRVCSLRMNR LAGVGWRVDY TLSSSLLQSV EEPMVHLRLE VAAAPGTPAQ PVAMSLSADK FQVLLAELKQ AQTLMSSLG

UniProtKB: COMM domain-containing protein 4

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Macromolecule #5: COMMD5

MacromoleculeName: COMMD5 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSAVGAATPY LHHPGDSHSG RVSFLGAQLP PEVAAMARLL GDLDRSTFRK LLKFVVSSLQ GEDCREAVQR LGVSANLPEE QLGALLAGMH TLLQQALRLP PTSLKPDTFR DQLQELCIPQ DLVGDLASVV FGSQRPLLDS VAQQQGAWLP HVADFRWRVD VAISTSALAR ...String:
MSAVGAATPY LHHPGDSHSG RVSFLGAQLP PEVAAMARLL GDLDRSTFRK LLKFVVSSLQ GEDCREAVQR LGVSANLPEE QLGALLAGMH TLLQQALRLP PTSLKPDTFR DQLQELCIPQ DLVGDLASVV FGSQRPLLDS VAQQQGAWLP HVADFRWRVD VAISTSALAR SLQPSVLMQL KLSDGSAYRF EVPTAKFQEL RYSVALVLKE MADLEKRCER RLQD

UniProtKB: COMM domain-containing protein 5

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Macromolecule #6: COMMD6

MacromoleculeName: COMMD6 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MEASSEPPLD AKSDVTNQLV DFQWKLGMAV SSDTCRSLKY PYVAVMLKVA DHSGQVKTKC FEMTIPQFQN FYRQFKEIAA VIETV

UniProtKB: COMM domain-containing protein 6

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Macromolecule #7: COMMD7

MacromoleculeName: COMMD7 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGRLHCTEDP VPEAVGGDMQ QLNQLGAQQF SALTEVLFHF LTEPKEVERF LAQLSEFATT NQISLGSLRS IVKSLLLVPN GALKKSLTAK QVQADFITLG LSEEKATYFS EKWKQNAPTL ARWAIGQTLM INQLIDMEWK FGVTSGSSEL EKVGSIFLQL KLVVKKGNQT ...String:
MGRLHCTEDP VPEAVGGDMQ QLNQLGAQQF SALTEVLFHF LTEPKEVERF LAQLSEFATT NQISLGSLRS IVKSLLLVPN GALKKSLTAK QVQADFITLG LSEEKATYFS EKWKQNAPTL ARWAIGQTLM INQLIDMEWK FGVTSGSSEL EKVGSIFLQL KLVVKKGNQT ENVYIELTLP QFYSFLHEME RVRTSMECFC

UniProtKB: COMM domain-containing protein 7

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Macromolecule #8: COMMD8

MacromoleculeName: COMMD8 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MEPEEGTPLW RLQKLPAELG PQLLHKIIDG ICGRAYPVYQ DYHTVWESEE WMHVLEDIAK FFKAIVGKNL PDEEIFQQLN QLNSLHQETI MKCVKSRKDE IKQALSREIV AISSAQLQDF DWQVKLALSS DKIAALRMPL LSLHLDVKEN GEVKPYSIEM SREELQNLIQ SLEAANKVVL QLK

UniProtKB: COMM domain-containing protein 8

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Macromolecule #9: COMMD9

MacromoleculeName: COMMD9 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAALTAEHFA ALQSLLKASS KDVVRQLCQE SFSSSALGLK KLLDVTCSSL SVTQEEAEEL LQALHRLTRL VAFRDLSSAE AILALFPENF HQNLKNLLTK IILEHVSTWR TEAQANQISL PRLVDLDWRV DIKTSSDSIS RMAVPTCLLQ MKIQEDPSLC GDKPSISAVT ...String:
MAALTAEHFA ALQSLLKASS KDVVRQLCQE SFSSSALGLK KLLDVTCSSL SVTQEEAEEL LQALHRLTRL VAFRDLSSAE AILALFPENF HQNLKNLLTK IILEHVSTWR TEAQANQISL PRLVDLDWRV DIKTSSDSIS RMAVPTCLLQ MKIQEDPSLC GDKPSISAVT VELSKETLDT MLDGLGRIRD QLSAVASK

UniProtKB: COMM domain-containing protein 9

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Macromolecule #10: COMMD10

MacromoleculeName: COMMD10 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAVPAALILR ESPSMKKAVS LINAIDTGRF PRLLTRILQK LHLKAESSFS EEEEEKLQAA FSLEKQDLHL VLETISFILE QAVYHNVKPA ALQQQLENIH LRQDKAEAFV NTWSSMGQET VEKFRQRILA PCKLETVGWQ LNLQMAHSAQ AKLKSPQAVL QLGVNNEDSK ...String:
MAVPAALILR ESPSMKKAVS LINAIDTGRF PRLLTRILQK LHLKAESSFS EEEEEKLQAA FSLEKQDLHL VLETISFILE QAVYHNVKPA ALQQQLENIH LRQDKAEAFV NTWSSMGQET VEKFRQRILA PCKLETVGWQ LNLQMAHSAQ AKLKSPQAVL QLGVNNEDSK SLEKVLVEFS HKELFDFYNK LETIQAQLDS LT

UniProtKB: COMM domain-containing protein 10

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Macromolecule #11: CCDC93

MacromoleculeName: CCDC93 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEKI VSVLPRMKCP HQLEPHQIQG MDFIHIFPVV QWLVKRAIET KEEMGDYIRS YSVSQFQKTY SLPEDDDFIK RKEKAIKTVV ...String:
MGLPRGPEGQ GLPEVETRED EEQNVKLTEI LELLVAAGYF RARIKGLSPF DKVVGGMTWC ITTCNFDVDV DLLFQENSTI GQKIALSEKI VSVLPRMKCP HQLEPHQIQG MDFIHIFPVV QWLVKRAIET KEEMGDYIRS YSVSQFQKTY SLPEDDDFIK RKEKAIKTVV DLSEVYKPRR KYKRHQGAEE LLDEESRIHA TLLEYGRRYG FSRQSKMEKA EDKKTALPAG LSATEKADAH EEDELRAAEE QRIQSLMTKM TAMANEESRL TASSVGQIVG LCSAEIKQIV SEYAEKQSEL SAEESPEKLG TSQLHRRKVI SLNKQIAQKT KHLEELRASH TSLQARYNEA KKTLTELKTY SEKLDKEQAA LEKIESKADP SILQNLRALV AMNENLKSQE QEFKAHCREE MTRLQQEIEN LKAERAPRGD EKTLSSGEPP GTLTSAMTHD EDLDRRYNME KEKLYKIRLL QARRNREIAI LHRKIDEVPS RAELIQYQKR FIELYRQISA VHKETKQFFT LYNTLDDKKV YLEKEISLLN SIHENFSQAM ASPAARDQFL RQMEQIVEGI KQSRMKMEKK KQENKMRRDQ LNDQYLELLE KQRLYFKTVK EFKEEGRKNE MLLSKVKAKA S

UniProtKB: Coiled-coil domain-containing protein 93

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Macromolecule #12: CCDC22

MacromoleculeName: CCDC22 / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNFL YPSEPDLRDL LLFLAERLPT DASEDADQPA GDSAILLRAI GSQIRDQLAL PWVPPHLRTP KLQHLQGSAL QKPFHASRLV ...String:
MEEADRILIH SLRQAGTAVP PDVQTLRAFT TELVVEAVVR CLRVINPAVG SGLSPLLPLA MSARFRLAMS LAQACMDLGY PLELGYQNFL YPSEPDLRDL LLFLAERLPT DASEDADQPA GDSAILLRAI GSQIRDQLAL PWVPPHLRTP KLQHLQGSAL QKPFHASRLV VPELSSRGEP REFQASPLLL PVPTQVPQPV GRVASLLEHH ALQLCQQTGR DRPGDEDWVH RTSRLPPQED TRAQRQRLQK QLTEHLRQSW GLLGAPIQAR DLGELLQAWG AGAKTGAPKG SRFTHSEKFT FHLEPQAQAT QVSDVPATSR RPEQVTWAAQ EQELESLREQ LEGVNRSIEE VEADMKTLGV SFVQAESECR HSKLSTAERE QALRLKSRAV ELLPDGTANL AKLQLVVENS AQRVIHLAGQ WEKHRVPLLA EYRHLRKLQD CRELESSRRL AEIQELHQSV RAAAEEARRK EEVYKQLMSE LETLPRDVSR LAYTQRILEI VGNIRKQKEE ITKILSDTKE LQKEINSLSG KLDRTFAVTD ELVFKDAKKD DAVRKAYKYL AALHENCSQL IQTIEDTGTI MREVRDLEEQ IETELGKKTL SNLEKIREDY RALRQENAGL LGRVREA

UniProtKB: Coiled-coil domain-containing protein 22

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Macromolecule #13: VPS29

MacromoleculeName: VPS29 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQV IPWGDMASLA LLQRQFDVDI LISGHTHKFE AFEHENKFYI NPGSATGAYN ALETNIIPSF VLMDIQASTV VTYVYQLIGD DVKVERIEYK KP

UniProtKB: Vacuolar protein sorting-associated protein 29

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Macromolecule #14: VPS35L

MacromoleculeName: VPS35L / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPAA LAAAMDSSRR KRDRDDNSVV GSDFEPWTNK RGEILARYTT TEKLSINLFM GSEKGKAGTA TLAMSEKVRT RLEELDDFEE ...String:
MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPAA LAAAMDSSRR KRDRDDNSVV GSDFEPWTNK RGEILARYTT TEKLSINLFM GSEKGKAGTA TLAMSEKVRT RLEELDDFEE GSQKELLNLT QQDYVNRIEE LNQSLKDAWA SDQKVKALKI VIQCSKLLSD TSVIQFYPSK FVLITDILDT FGKLVYERIF SMCVDSRSVL PDHFSPENAN DTAKETCLNW FFKIASIREL IPRFYVEASI LKCNKFLSKT GISECLPRLT CMIRGIGDPL VSVYARAYLC RVGMEVAPHL KETLNKNFFD FLLTFKQIHG DTVQNQLVVQ GVELPSYLPL YPPAMDWIFQ CISYHAPEAL LTEMMERCKK LGNNALLLNS VMSAFRAEFI ATRSMDFIGM IKECDESGFP KHLLFRSLGL NLALADPPES DRLQILNEAW KVITKLKNPQ DYINCAEVWV EYTCKHFTKR EVNTVLADVI KHMTPDRAFE DSYPQLQLII KKVIAHFHDF SVLFSVEKFL PFLDMFQKES VRVEVCKCIM DAFIKHQQEP TKDPVILNAL LHVCKTMHDS VNALTLEDEK RMLSYLINGF IKMVSFGRDF EQQLSFYVES RSMFCNLEPV LVQLIHSVNR LAMETRKVMK GNHSRKTAAF VRACVAYCFI TIPSLAGIFT RLNLYLHSGQ VALANQCLSQ ADAFFKAAIS LVPEVPKMIN IDGKMRPSES FLLEFLCNFF STLLIVPDHP EHGVLFLVRE LLNVIQDYTW EDNSDEKIRI YTCVLHLLSA MSQETYLYHI DKVDSNDSLY GGDSKFLAEN NKLCETVMAQ ILEHLKTLAK DEALKRQSSL GLSFFNSILA HGDLRNNKLN QLSVNLWHLA QRHGCADTRT MVKTLEYIKK QSKQPDMTHL TELALRLPLQ TRT

UniProtKB: VPS35 endosomal protein-sorting factor-like

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Macromolecule #15: VPS26C

MacromoleculeName: VPS26C / type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGTALDIKIK RANKVYHAGE VLSGVVVISS KDSVQHQGVS LTMEGTVNLQ LSAKSVGVFE AFYNSVKPIQ IINSTIEMVK PGKFPSGKTE IPFEFPLHLK GNKVLYETYH GVFVNIQYTL RCDMKRSLLA KDLTKTCEFI VHSAPQKGKF TPSPVDFTIT PETLQNVKER ...String:
MGTALDIKIK RANKVYHAGE VLSGVVVISS KDSVQHQGVS LTMEGTVNLQ LSAKSVGVFE AFYNSVKPIQ IINSTIEMVK PGKFPSGKTE IPFEFPLHLK GNKVLYETYH GVFVNIQYTL RCDMKRSLLA KDLTKTCEFI VHSAPQKGKF TPSPVDFTIT PETLQNVKER ALLPKFLLRG HLNSTNCVIT QPLTGELVVE SSEAAIRSVE LQLVRVETCG CAEGYARDAT EIQNIQIADG DVCRGLSVPI YMVFPRLFTC PTLETTNFKV EFEVNIVVLL HPDHLITENF PLKLCRI

UniProtKB: Vacuolar protein sorting-associated protein 26C

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Macromolecule #16: DENND10

MacromoleculeName: DENND10 / type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAAAEVADTQ LMLGVGLIEK DTNGEVLWVW CYPSTTATLR NLLLRKCCLT DENKLLHPFV FGQYRRTWFY ITTIEVPDSS ILKKVTHFSI VLTAKDFNPE KYAAFTRILC RMYLKHGSPV KMMESYIAVL TKGICQSEEN GSFLSKDFDA RKAYLAGSIK DIVSQFGMET ...String:
MAAAEVADTQ LMLGVGLIEK DTNGEVLWVW CYPSTTATLR NLLLRKCCLT DENKLLHPFV FGQYRRTWFY ITTIEVPDSS ILKKVTHFSI VLTAKDFNPE KYAAFTRILC RMYLKHGSPV KMMESYIAVL TKGICQSEEN GSFLSKDFDA RKAYLAGSIK DIVSQFGMET VILHTALMLK KRIVVYHPKI EAVQEFTRTL PALVWHRQDW TILHSYVHLN ADELEALQMC TGYVAGFVDL EVSNRPDLYD VFVNLAESEI TIAPLAKEAM AMGKLHKEMG QLIVQSAEDP EKSESHVIQD IALKTREIFT NLAPFSEVSA DGEKRVLNLE ALKQKRFPPA TENFLYHLAA AEQMLKI

UniProtKB: DENN domain-containing protein 10

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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: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Number grids imaged: 1 / Number real images: 5884 / Average electron dose: 42.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 340000
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 90000
FSC plot (resolution estimation)

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