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- EMDB-23827: Structure of C9orf72:SMCR8:WDR41 in complex with ARF1 -

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Basic information

Entry
Database: EMDB / ID: EMD-23827
TitleStructure of C9orf72:SMCR8:WDR41 in complex with ARF1
Map datapostprocess with deepemhancer "tightTarget" model
Sample
  • Complex: Complex of C9orf72:SMCR8:WDR41 with ARF1
    • Protein or peptide: WD repeat-containing protein 41
    • Protein or peptide: Guanine nucleotide exchange protein SMCR8
    • Protein or peptide: Guanine nucleotide exchange C9orf72
    • Protein or peptide: ADP-ribosylation factor 1ARF1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Atg1/ULK1 kinase complex / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / late endosome to lysosome transport / Intra-Golgi traffic / regulation of TORC1 signaling / Synthesis of PIPs at the Golgi membrane / regulation of autophagosome assembly ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Atg1/ULK1 kinase complex / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / late endosome to lysosome transport / Intra-Golgi traffic / regulation of TORC1 signaling / Synthesis of PIPs at the Golgi membrane / regulation of autophagosome assembly / negative regulation of autophagosome assembly / regulation of actin filament organization / guanyl-nucleotide exchange factor complex / negative regulation of immune response / Nef Mediated CD4 Down-regulation / dendritic spine organization / axon extension / negative regulation of exocytosis / Flemming body / positive regulation of autophagosome maturation / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / main axon / Lysosome Vesicle Biogenesis / negative regulation of macroautophagy / Golgi Associated Vesicle Biogenesis / protein kinase inhibitor activity / cell leading edge / Synthesis of PIPs at the plasma membrane / positive regulation of macroautophagy / intracellular copper ion homeostasis / autophagosome / positive regulation of TOR signaling / COPI-mediated anterograde transport / axonal growth cone / stress granule assembly / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / sarcomere / guanyl-nucleotide exchange factor activity / small monomeric GTPase / negative regulation of protein phosphorylation / cell projection / regulation of autophagy / P-body / intracellular protein transport / negative regulation of protein kinase activity / small GTPase binding / cellular response to virus / autophagy / positive regulation of GTPase activity / endocytosis / cytoplasmic stress granule / regulation of protein localization / presynapse / perikaryon / postsynapse / nuclear membrane / postsynaptic density / lysosome / endosome / neuron projection / lysosomal membrane / protein domain specific binding / Golgi membrane / negative regulation of gene expression / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / dendrite / chromatin / GTP binding / protein kinase binding / magnesium ion binding / protein-containing complex / extracellular space / RNA binding / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
WD repeat-containing protein 41 / Guanine nucleotide exchange factor C9orf72 / C9orf72-like protein family / Tripartite DENN C9ORF72-type domain profile. / Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. / ADP-ribosylation factor 1-5 / small GTPase Arf family profile. ...WD repeat-containing protein 41 / Guanine nucleotide exchange factor C9orf72 / C9orf72-like protein family / Tripartite DENN C9ORF72-type domain profile. / Folliculin/SMCR8, longin domain / Folliculin/SMCR8, tripartite DENN domain / Vesicle coat protein involved in Golgi to plasma membrane transport / Tripartite DENN FLCN/SMCR8-type domain profile. / ADP-ribosylation factor 1-5 / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADP-ribosylation factor 1 / Guanine nucleotide exchange protein SMCR8 / Guanine nucleotide exchange factor C9orf72 / WD repeat-containing protein 41
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsSu M-Y / Hurley JH
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH2010086 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for the ARF GAP activity and specificity of the C9orf72 complex.
Authors: Ming-Yuan Su / Simon A Fromm / Jonathan Remis / Daniel B Toso / James H Hurley /
Abstract: Mutation of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 ...Mutation of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 forms a complex with SMCR8 and WDR41, which was reported to have GTPase activating protein activity toward ARF proteins, RAB8A, and RAB11A. We determined the cryo-EM structure of ARF1-GDP-BeF bound to C9orf72:SMCR8:WDR41. The SMCR8 and C9orf72 domains form the binding pocket for ARF1. One face of the C9orf72 domain holds ARF1 in place, while the SMCR8 positions the catalytic finger Arg147 in the ARF1 active site. Mutations in interfacial residues of ARF1 and C9orf72 reduced or eliminated GAP activity. RAB8A GAP required ~10-fold higher concentrations of the C9orf72 complex than for ARF1. These data support a specific function for the C9orf72 complex as an ARF GAP. The structure also provides a model for the active forms of the longin domain GAPs of FLCN and NPRL2 that regulate the Rag GTPases of the mTORC1 pathway.
History
DepositionApr 12, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.27
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.27
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mge
  • Surface level: 0.27
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23827.png

Downloads & links

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Map

FileDownload / File: emd_23827.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess with deepemhancer "tightTarget" model
Voxel sizeX=Y=Z: 0.94 Å
Density
Contour LevelBy AUTHOR: 0.27 / Movie #1: 0.27
Minimum - Maximum-0.001730138 - 1.9661589
Average (Standard dev.)0.00237881 (±0.035833158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 248.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.940.940.94
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z248.160248.160248.160
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.0021.9660.002

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Supplemental data

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Sample components

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Entire : Complex of C9orf72:SMCR8:WDR41 with ARF1

EntireName: Complex of C9orf72:SMCR8:WDR41 with ARF1
Components
  • Complex: Complex of C9orf72:SMCR8:WDR41 with ARF1
    • Protein or peptide: WD repeat-containing protein 41
    • Protein or peptide: Guanine nucleotide exchange protein SMCR8
    • Protein or peptide: Guanine nucleotide exchange C9orf72
    • Protein or peptide: ADP-ribosylation factor 1ARF1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of C9orf72:SMCR8:WDR41 with ARF1

SupramoleculeName: Complex of C9orf72:SMCR8:WDR41 with ARF1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: WD repeat-containing protein 41

MacromoleculeName: WD repeat-containing protein 41 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.783805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLRWLIGGGR EPQGLAEKSP LQTIGEEQTQ NPYTELLVLK AHHDIVRFLV QLDDYRFASA GDDGIVVVWN AQTGEKLLEL NGHTQKITA IITFPSLESC EEKNQLILTA SADRTVIVWD GDTTRQVQRI SCFQSTVKCL TVLQRLDVWL SGGNDLCVWN R KLDLLCKT ...String:
MLRWLIGGGR EPQGLAEKSP LQTIGEEQTQ NPYTELLVLK AHHDIVRFLV QLDDYRFASA GDDGIVVVWN AQTGEKLLEL NGHTQKITA IITFPSLESC EEKNQLILTA SADRTVIVWD GDTTRQVQRI SCFQSTVKCL TVLQRLDVWL SGGNDLCVWN R KLDLLCKT SHLSDTGISA LVEIPKNCVV AAVGKELIIF RLVAPTEGSL EWDILEVKRL LDHQDNILSL INVNDLSFVT GS HVGELII WDALDWTMQA YERNFWDPSP QLDTQQEIKL CQKSNDISIH HFTCDEENVF AAVGRGLYVY SLQMKRVIAC QKT AHDSNV LHVARLPNRQ LISCSEDGSV RIWELREKQQ LAAEPVPTGF FNMWGFGRVS KQASQPVKKQ QENATSCSLE LIGD LIGHS SSVEMFLYFE DHGLVTCSAD HLIILWKNGE RESGLRSLRL FQKLEENGDL YLAV

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Macromolecule #2: Guanine nucleotide exchange protein SMCR8

MacromoleculeName: Guanine nucleotide exchange protein SMCR8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.149094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MISAPDVVAF TKEEEYEEEP YNEPALPEEY SVPLFPFASQ GANPWSKLSG AKFSRDFILI SEFSEQVGPQ PLLTIPNDTK VFGTFDLNY FSLRIMSVDY QASFVGHPPG SAYPKLNFVE DSKVVLGDSK EGAFAYVHHL TLYDLEARGF VRPFCMAYIS A DQHKIMQQ ...String:
MISAPDVVAF TKEEEYEEEP YNEPALPEEY SVPLFPFASQ GANPWSKLSG AKFSRDFILI SEFSEQVGPQ PLLTIPNDTK VFGTFDLNY FSLRIMSVDY QASFVGHPPG SAYPKLNFVE DSKVVLGDSK EGAFAYVHHL TLYDLEARGF VRPFCMAYIS A DQHKIMQQ FQELSAEFSR ASECLKTGNR KAFAGELEKK LKDLDYTRTV LHTETEIQKK ANDKGFYSSQ AIEKANELAS VE KSIIEHQ DLLKQIRSYP HRKLKGHDLC PGEMEHIQDQ ASQASTTSNP DESADTDLYT CRPAYTPKLI KAKSTKCFDK KLK TLEELC DTEYFTQTLA QLSHIEHMFR GDLCYLLTSQ IDRALLKQQH ITNFLFEDFV EVDDRMVEKQ ESIPSKPSQD RPPS SSLEE CPIPKVLISV GSYKSSVESV LIKMEQELGD EEYKEVEVTE LSSFDPQENL DYLDMDMKGS ISSGESIEVL GTEKS TSVL SKSDSQASLT VPLSPQVVRS KAVSHRTISE DSIEVLSTCP SEALIPDDFK ASYPSAINEE ESYPDGNEGA IRFQAS ISP PELGETEEGS IENTPSQIDS SCCIGKESDG QLVLPSTPAH THSDEDGVVS SPPQRHRQKD QGFRVDFSVE NANPSSR DN SCEGFPAYEL DPSHLLASRD ISKTSLDNYS DTTSYVSSVA STSSDRIPSA YPAGLSSDRH KKRAGQNALK FIRQYPFA H PAIYSLLSGR TLVVLGEDEA IVRKLVTALA IFVPSYGCYA KPVKHWASSP LHIMDFQKWK LIGLQRVASP AGAGTLHAL SRYSRYTSIL DLDNKTLRCP LYRGTLVPRL ADHRTQIKRG STYYLHVQSM LTQLCSKAFL YTFCHHLHLP THDKETEELV ASRQMSFLK LTLGLVNEDV RVVQYLAELL KLHYMQESPG TSHPMLRFDY VPSFLYKI

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Macromolecule #3: Guanine nucleotide exchange C9orf72

MacromoleculeName: Guanine nucleotide exchange C9orf72 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.391477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTLCPPPSP AVAKTEIALS GKSPLLAATF AYWDNILGPR VRHIWAPKTE QVLLSDGEIT FLANHTLNGE ILRNAESGAI DVKFFVLSE KGVIIVSLIF DGNWNGDRST YGLSIILPQT ELSFYLPLHR VCVDRLTHII RKGRIWMHKE RQENVQKIIL E GTERMEDQ ...String:
MSTLCPPPSP AVAKTEIALS GKSPLLAATF AYWDNILGPR VRHIWAPKTE QVLLSDGEIT FLANHTLNGE ILRNAESGAI DVKFFVLSE KGVIIVSLIF DGNWNGDRST YGLSIILPQT ELSFYLPLHR VCVDRLTHII RKGRIWMHKE RQENVQKIIL E GTERMEDQ GQSIIPMLTG EVIPVMELLS SMKSHSVPEE IDIADTVLND DDIGDSCHEG FLLNAISSHL QTCGCSVVVG SS AEKVNKI VRTLCLFLTP AERKCSRLCE AESSFKYESG LFVQGLLKDS TGSFVLPFRQ VMYAPYPTTH IDVDVNTVKQ MPP CHEHIY NQRRYMRSEL TAFWRATSEE DMAQDTIIYT DESFTPDLNI FQDVLHRDTL VKAFLDQVFQ LKPGLSLRST FLAQ FLLVL HRKALTLIKY IEDDTQKGKK PFKSLRNLKI DLDLTAEGDL NIIMALAEKI KPGLHSFIFG RPFYTSVQER DVLMT F

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Macromolecule #4: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.994572 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ATEMRILMVG LDAAGKTTIL YKLKLGEIVT TIPTIGFNVE TVEYKNISFT VWDVGGQDKI RPLWRHYFQN TQGLIFVVDS NDRERVNEA REELMRMLAE DELRDAVLLV FANKQDLPNA MNAAEITDKL GLHSLRHRNW YIQATCATSG DGLYEGLDWL S NQLRNQ

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #6: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.16 mg/mL
BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsconcentration range of 0.16-0.2 mg/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 796219

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7mge:
Structure of C9orf72:SMCR8:WDR41 in complex with ARF1

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