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- EMDB-17340: Structure of the human Commander complex COMMD ring -

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Basic information

Entry
Database: EMDB / ID: EMD-17340
TitleStructure of the human Commander complex COMMD ring
Map data
Sample
  • Complex: Human Commander Complex
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
KeywordsCOMMD fold / calponin homology fold / pseudo-C5 symmetry / UNKNOWN FUNCTION
Function / homology
Function and homology information


negative regulation of sodium ion transmembrane transport / plasma membrane to endosome transport / cytoplasmic sequestering of NF-kappaB / regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 ...negative regulation of sodium ion transmembrane transport / plasma membrane to endosome transport / cytoplasmic sequestering of NF-kappaB / regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / phosphatidylinositol-3,5-bisphosphate binding / Cul2-RING ubiquitin ligase complex / sodium ion transport / negative regulation of NF-kappaB transcription factor activity / cullin family protein binding / phosphatidylinositol-3,4,5-trisphosphate binding / 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 / cholesterol homeostasis / positive regulation of protein ubiquitination / nucleotide-excision repair / recycling endosome / protein transport / 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 / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / : ...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 / : / COMMD1 N-terminal domain / COMMD protein 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, 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_17340.png

Downloads & links

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Map

FileDownload / File: emd_17340.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 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

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.6538875 - 2.4025207
Average (Standard dev.)-0.00014474554 (±0.026476901)
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_17340_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17340_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17340_half_map_2.map
Projections & Slices
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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: COMM domain-containing protein 1
    • Protein or peptide: COMM domain-containing protein 2
    • Protein or peptide: COMM domain-containing protein 3
    • Protein or peptide: COMM domain-containing protein 4
    • Protein or peptide: COMM domain-containing protein 5
    • Protein or peptide: COMM domain-containing protein 6
    • Protein or peptide: COMM domain-containing protein 7
    • Protein or peptide: COMM domain-containing protein 8
    • Protein or peptide: COMM domain-containing protein 9
    • Protein or peptide: COMM domain-containing protein 10
    • Protein or peptide: Coiled-coil domain-containing protein 93
    • Protein or peptide: Coiled-coil domain-containing protein 22
  • Ligand: water

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Supramolecule #1: Human Commander Complex

SupramoleculeName: Human Commander Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 560 KDa

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Macromolecule #1: COMM domain-containing protein 1

MacromoleculeName: COMM domain-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.203061 KDa
SequenceString:
MAAGELEGGK PLSGLLNALA QDTFHGYPGI TEELLRSQLY PEVPPEEFRP FLAKMRGILK SIASADMDFN QLEAFLTAQT KKQGGITSD QAAVISKFWK SHKTKIRESL MNQSRWNSGL RGLSWRVDGK SQSRHSAQIH TPVAIIELEL GKYGQESEFL C LEFDEVKV NQILKTLSEV EESISTLISQ PN

UniProtKB: COMM domain-containing protein 1

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Macromolecule #2: COMM domain-containing protein 2

MacromoleculeName: COMM domain-containing protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.776113 KDa
SequenceString: MLLELSEEHK EHLAFLPQVD SAVVAEFGRI AVEFLRRGAN PKIYEGAARK LNVSSDTVQH GVEGLTYLLT ESSKLMISEL DFQDSVFVL GFSEELNKLL LQLYLDNRKE IRTILSELAP SLPSYHNLEW RLDVQLASRS LRQQIKPAVT IKLHLNQNGD H NTKVLQTD ...String:
MLLELSEEHK EHLAFLPQVD SAVVAEFGRI AVEFLRRGAN PKIYEGAARK LNVSSDTVQH GVEGLTYLLT ESSKLMISEL DFQDSVFVL GFSEELNKLL LQLYLDNRKE IRTILSELAP SLPSYHNLEW RLDVQLASRS LRQQIKPAVT IKLHLNQNGD H NTKVLQTD PATLLHLVQQ LEQALEEMKT NHCRRVVRNI K

UniProtKB: COMM domain-containing protein 2

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Macromolecule #3: COMM domain-containing protein 3

MacromoleculeName: COMM domain-containing protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.179117 KDa
SequenceString: MELSESVQKG FQMLADPRSF DSNAFTLLLR AAFQSLLDAQ ADEAVLDHPD LKHIDPVVLK HCHAAAATYI LEAGKHRADK STLSTYLED CKFDRERIEL FCTEYQNNKN SLEILLGSIG RSLPHITDVS WRLEYQIKTN QLHRMYRPAY LVTLSVQNTD S PSYPEISF ...String:
MELSESVQKG FQMLADPRSF DSNAFTLLLR AAFQSLLDAQ ADEAVLDHPD LKHIDPVVLK HCHAAAATYI LEAGKHRADK STLSTYLED CKFDRERIEL FCTEYQNNKN SLEILLGSIG RSLPHITDVS WRLEYQIKTN QLHRMYRPAY LVTLSVQNTD S PSYPEISF SCSMEQLQDL VGKLKDASKS LERATQL

UniProtKB: COMM domain-containing protein 3

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Macromolecule #4: COMM domain-containing protein 4

MacromoleculeName: COMM domain-containing protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.790354 KDa
SequenceString: MRFRFCGDLD CPDWVLAEIS TLAKMSSVKL RLLCSQVLKE LLGQGIDYEK ILKLTADAKF ESGDVKATVA VLSFILSSAA KHSVDGESL SSELQQLGLP KEHAASLCRC YEEKQSPLQK HLRVCSLRMN RLAGVGWRVD YTLSSSLLQS VEEPMVHLRL E VAAAPGTP ...String:
MRFRFCGDLD CPDWVLAEIS TLAKMSSVKL RLLCSQVLKE LLGQGIDYEK ILKLTADAKF ESGDVKATVA VLSFILSSAA KHSVDGESL SSELQQLGLP KEHAASLCRC YEEKQSPLQK HLRVCSLRMN RLAGVGWRVD YTLSSSLLQS VEEPMVHLRL E VAAAPGTP AQPVAMSLSA DKFQVLLAEL KQAQTLMSSL G

UniProtKB: COMM domain-containing protein 4

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Macromolecule #5: COMM domain-containing protein 5

MacromoleculeName: COMM domain-containing protein 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.699361 KDa
SequenceString: MSAVGAATPY LHHPGDSHSG RVSFLGAQLP PEVAAMARLL GDLDRSTFRK LLKFVVSSLQ GEDCREAVQR LGVSANLPEE QLGALLAGM HTLLQQALRL PPTSLKPDTF RDQLQELCIP QDLVGDLASV VFGSQRPLLD SVAQQQGAWL PHVADFRWRV D VAISTSAL ...String:
MSAVGAATPY LHHPGDSHSG RVSFLGAQLP PEVAAMARLL GDLDRSTFRK LLKFVVSSLQ GEDCREAVQR LGVSANLPEE QLGALLAGM HTLLQQALRL PPTSLKPDTF RDQLQELCIP QDLVGDLASV VFGSQRPLLD SVAQQQGAWL PHVADFRWRV D VAISTSAL ARSLQPSVLM QLKLSDGSAY RFEVPTAKFQ ELRYSVALVL KEMADLEKRC ERRLQD

UniProtKB: COMM domain-containing protein 5

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Macromolecule #6: COMM domain-containing protein 6

MacromoleculeName: COMM domain-containing protein 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.648074 KDa
SequenceString:
MEASSEPPLD AKSDVTNQLV DFQWKLGMAV SSDTCRSLKY PYVAVMLKVA DHSGQVKTKC FEMTIPQFQN FYRQFKEIAA VIETV

UniProtKB: COMM domain-containing protein 6

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Macromolecule #7: COMM domain-containing protein 7

MacromoleculeName: COMM domain-containing protein 7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.561953 KDa
SequenceString: MGRLHCTEDP VPEAVGGDMQ QLNQLGAQQF SALTEVLFHF LTEPKEVERF LAQLSEFATT NQISLGSLRS IVKSLLLVPN GALKKSLTA KQVQADFITL GLSEEKATYF SEKWKQNAPT LARWAIGQTL MINQLIDMEW KFGVTSGSSE LEKVGSIFLQ L KLVVKKGN ...String:
MGRLHCTEDP VPEAVGGDMQ QLNQLGAQQF SALTEVLFHF LTEPKEVERF LAQLSEFATT NQISLGSLRS IVKSLLLVPN GALKKSLTA KQVQADFITL GLSEEKATYF SEKWKQNAPT LARWAIGQTL MINQLIDMEW KFGVTSGSSE LEKVGSIFLQ L KLVVKKGN QTENVYIELT LPQFYSFLHE MERVRTSMEC FC

UniProtKB: COMM domain-containing protein 7

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Macromolecule #8: COMM domain-containing protein 8

MacromoleculeName: COMM domain-containing protein 8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.116342 KDa
SequenceString:
MEPEEGTPLW RLQKLPAELG PQLLHKIIDG ICGRAYPVYQ DYHTVWESEE WMHVLEDIAK FFKAIVGKNL PDEEIFQQLN QLNSLHQET IMKCVKSRKD EIKQALSREI VAISSAQLQD FDWQVKLALS SDKIAALRMP LLSLHLDVKE NGEVKPYSIE M SREELQNL IQSLEAANKV VLQLK

UniProtKB: COMM domain-containing protein 8

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Macromolecule #9: COMM domain-containing protein 9

MacromoleculeName: COMM domain-containing protein 9 / type: protein_or_peptide / ID: 9 / Details: Bait for capturing the endogenous complex / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.844117 KDa
SequenceString: MAALTAEHFA ALQSLLKASS KDVVRQLCQE SFSSSALGLK KLLDVTCSSL SVTQEEAEEL LQALHRLTRL VAFRDLSSAE AILALFPEN FHQNLKNLLT KIILEHVSTW RTEAQANQIS LPRLVDLDWR VDIKTSSDSI SRMAVPTCLL QMKIQEDPSL C GDKPSISA ...String:
MAALTAEHFA ALQSLLKASS KDVVRQLCQE SFSSSALGLK KLLDVTCSSL SVTQEEAEEL LQALHRLTRL VAFRDLSSAE AILALFPEN FHQNLKNLLT KIILEHVSTW RTEAQANQIS LPRLVDLDWR VDIKTSSDSI SRMAVPTCLL QMKIQEDPSL C GDKPSISA VTVELSKETL DTMLDGLGRI RDQLSAVASK

UniProtKB: COMM domain-containing protein 9

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Macromolecule #10: COMM domain-containing protein 10

MacromoleculeName: COMM domain-containing protein 10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.995402 KDa
SequenceString: MAVPAALILR ESPSMKKAVS LINAIDTGRF PRLLTRILQK LHLKAESSFS EEEEEKLQAA FSLEKQDLHL VLETISFILE QAVYHNVKP AALQQQLENI HLRQDKAEAF VNTWSSMGQE TVEKFRQRIL APCKLETVGW QLNLQMAHSA QAKLKSPQAV L QLGVNNED ...String:
MAVPAALILR ESPSMKKAVS LINAIDTGRF PRLLTRILQK LHLKAESSFS EEEEEKLQAA FSLEKQDLHL VLETISFILE QAVYHNVKP AALQQQLENI HLRQDKAEAF VNTWSSMGQE TVEKFRQRIL APCKLETVGW QLNLQMAHSA QAKLKSPQAV L QLGVNNED SKSLEKVLVE FSHKELFDFY NKLETIQAQL DSLT

UniProtKB: COMM domain-containing protein 10

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

MacromoleculeName: Coiled-coil domain-containing protein 93 / type: protein_or_peptide / ID: 11 / 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 #12: Coiled-coil domain-containing protein 22

MacromoleculeName: Coiled-coil domain-containing protein 22 / type: protein_or_peptide / ID: 12 / 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 #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 21 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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 - 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 667000
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-8p0w:
Structure of the human Commander complex COMMD ring

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