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- EMDB-45297: Structure of human ULK1C:PI3KC3-C1 supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-45297
TitleStructure of human ULK1C:PI3KC3-C1 supercomplex
Map data
Sample
  • Complex: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex
    • Protein or peptide: Phosphoinositide 3-kinase regulatory subunit 4
    • Protein or peptide: Phosphatidylinositol 3-kinase catalytic subunit type 3
    • Protein or peptide: Beclin 1-associated autophagy-related key regulator
    • Protein or peptide: Beclin-1
    • Protein or peptide: RB1-inducible coiled-coil protein 1
KeywordsAutophagy / Protein kinase / Lipid kinase / Supercomplex / IMMUNE SYSTEM
Function / homology
Function and homology information


extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / Toll Like Receptor 9 (TLR9) Cascade / postsynaptic endosome / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III ...extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / Toll Like Receptor 9 (TLR9) Cascade / postsynaptic endosome / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / engulfment of apoptotic cell / cellular response to oxygen-glucose deprivation / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / Atg1/ULK1 kinase complex / presynaptic endosome / positive regulation of stress granule assembly / ribophagy / glycophagy / response to mitochondrial depolarisation / positive regulation of protein lipidation / positive regulation by host of viral genome replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / mitochondria-associated endoplasmic reticulum membrane contact site / negative regulation of lysosome organization / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / regulation of protein complex stability / positive regulation of autophagosome assembly / phosphatidylinositol 3-kinase regulator activity / negative regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / protein localization to phagophore assembly site / receptor catabolic process / phagophore assembly site membrane / protein targeting to vacuole / SMAD protein signal transduction / protein targeting to lysosome / early endosome to late endosome transport / late endosome to vacuole transport / autophagy of mitochondrion / pexophagy / piecemeal microautophagy of the nucleus / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / negative regulation of programmed cell death / reticulophagy / response to iron(II) ion / phosphatidylinositol 3-kinase / lysosome organization / 1-phosphatidylinositol-3-kinase activity / mitotic metaphase chromosome alignment / post-transcriptional regulation of gene expression / cytoplasmic pattern recognition receptor signaling pathway / autophagosome membrane docking / endosome to lysosome transport / Macroautophagy / phosphatidylinositol-mediated signaling / positive regulation of cardiac muscle hypertrophy / RSV-host interactions / p38MAPK cascade / phosphatidylinositol phosphate biosynthetic process / autolysosome / regulation of protein phosphorylation / autophagosome membrane / negative regulation of protein phosphorylation / synaptic vesicle endocytosis / PI3K Cascade / axoneme / autophagosome assembly / RHO GTPases Activate NADPH Oxidases / response to vitamin E / autophagosome maturation / positive regulation of cell size / amyloid-beta metabolic process / regulation of macroautophagy / neuron development / phosphatidylinositol 3-kinase binding / cellular defense response / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / phagocytic vesicle / extrinsic apoptotic signaling pathway / JNK cascade / cellular response to copper ion / positive regulation of autophagy / cellular response to epidermal growth factor stimulus / cellular response to amino acid starvation / autophagosome / liver development / cellular response to starvation / regulation of cytokinesis / GABA-ergic synapse / negative regulation of extrinsic apoptotic signaling pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC
Similarity search - Function
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / : / VPS15-like, helical domain / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting ...UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / : / VPS15-like, helical domain / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Phosphatidylinositol 3-kinase, Vps34 type / HEAT repeat profile. / HEAT, type 2 / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Beclin-1 / Beclin 1-associated autophagy-related key regulator / Phosphatidylinositol 3-kinase catalytic subunit type 3 / RB1-inducible coiled-coil protein 1 / Phosphoinositide 3-kinase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.84 Å
AuthorsChen M / Hurley JH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111730 United States
Michael J. Fox FoundationASAP-000350 United States
Citation
Journal: Nat Struct Mol Biol / Year: 2025
Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex.
Authors: Minghao Chen / Thanh N Nguyen / Xuefeng Ren / Grace Khuu / Annan S I Cook / Yuanchang Zhao / Ahmet Yildiz / Michael Lazarou / James H Hurley /
Abstract: The Unc-51-like kinase protein kinase complex (ULK1C) is the most upstream and central player in the initiation of macroautophagy in mammals. Here, we determined the cryo-electron microscopy ...The Unc-51-like kinase protein kinase complex (ULK1C) is the most upstream and central player in the initiation of macroautophagy in mammals. Here, we determined the cryo-electron microscopy structure of the human ULK1C core at amino-acid-level resolution. We also determined a moderate-resolution structure of the ULK1C core in complex with another autophagy core complex, the class III phosphatidylinositol 3-OH kinase complex I (PI3KC3-C1). We show that the two complexes coassemble through extensive contacts between the FIP200 scaffold subunit of ULK1C and the VPS15, ATG14 and BECN1 subunits of PI3KC3-C1. The FIP200:ATG13:ULK1 core of ULK1C undergoes a rearrangement from 2:1:1 to 2:2:2 stoichiometry in the presence of PI3KC3-C1. This suggests a structural mechanism for the initiation of autophagy through formation of a ULK1C:PI3KC3-C1 supercomplex and dimerization of ULK1 on the FIP200 scaffold.
#1: Journal: bioRxiv / Year: 2023
Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
Authors: Chen M / Ren X / Cook A / Hurley JH
History
DepositionJun 11, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45297.png

Downloads & links

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Map

FileDownload / File: emd_45297.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 560 pix.
= 588. Å		1.05 Å/pix.
x 560 pix.
= 588. Å		1.05 Å/pix.
x 560 pix.
= 588. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0833
Minimum - Maximum-0.48397234 - 0.86900705
Average (Standard dev.)-0.00041187057 (±0.026046364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 588.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_45297_additional_1.map
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Half map: #1

Fileemd_45297_half_map_1.map
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Half map: #2

Fileemd_45297_half_map_2.map
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Sample components

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Entire : Supercomplex composed of ULK1 complex and PI3KC3-C1 complex

EntireName: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex
Components
  • Complex: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex
    • Protein or peptide: Phosphoinositide 3-kinase regulatory subunit 4
    • Protein or peptide: Phosphatidylinositol 3-kinase catalytic subunit type 3
    • Protein or peptide: Beclin 1-associated autophagy-related key regulator
    • Protein or peptide: Beclin-1
    • Protein or peptide: RB1-inducible coiled-coil protein 1

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Supramolecule #1: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex

SupramoleculeName: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Individually expressed the ULK1 complex core (consists of two molecules of FIP200 (1-640), ULK1 (828-1050), and ATG13 (363-517)) and the full-length PI3KC3-C1 (consists of VPS34, VPS15, ...Details: Individually expressed the ULK1 complex core (consists of two molecules of FIP200 (1-640), ULK1 (828-1050), and ATG13 (363-517)) and the full-length PI3KC3-C1 (consists of VPS34, VPS15, BECN1, and ATG14). Mixed the above two complexes in a molecular ratio of 1.5:1 and purified the supercomplex by strep pulldown of the TSF-tagged VPS15.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: Phosphoinositide 3-kinase regulatory subunit 4

MacromoleculeName: Phosphoinositide 3-kinase regulatory subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 153.293797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNQLAGIAP SQILSVESYF SDIHDFEYDK SLGSTRFFKV ARAKHREGLV VVKVFAIQDP TLPLTSYKQE LEELKIRLNS AQNCLPFQK ASEKASEKAA MLFRQYVRDN LYDRISTRPF LNNIEKRWIA FQILTAVDQA HKSGVRHGDI KTENVMVTSW N WVLLTDFA ...String:
MGNQLAGIAP SQILSVESYF SDIHDFEYDK SLGSTRFFKV ARAKHREGLV VVKVFAIQDP TLPLTSYKQE LEELKIRLNS AQNCLPFQK ASEKASEKAA MLFRQYVRDN LYDRISTRPF LNNIEKRWIA FQILTAVDQA HKSGVRHGDI KTENVMVTSW N WVLLTDFA SFKPTYLPED NPADFNYFFD TSRRRTCYIA PERFVDGGMF ATELEYMRDP STPLVDLNSN QRTRGELKRA MD IFSAGCV IAELFTEGVP LFDLSQLLAY RNGHFFPEQV LNKIEDHSIR ELVTQMIHRE PDKRLEAEDY LKQQRGNAFP EIF YTFLQP YMAQFAKETF LSADERILVI RKDLGNIIHN LCGHDLPEKA EGEPKENGLV ILVSVITSCL QTLKYCDSKL AALE LILHL APRLSVEILL DRITPYLLHF SNDSVPRVRA EALRTLTKVL ALVKEVPRND INIYPEYILP GIAHLAQDDA TIVRL AYAE NIALLAETAL RFLELVQLKN LNMENDPNNE EIDEVTHPNG NYDTELQALH EMVQQKVVTL LSDPENIVKQ TLMENG ITR LCVFFGRQKA NDVLLSHMIT FLNDKNDWHL RGAFFDSIVG VAAYVGWQSS SILKPLLQQG LSDAEEFVIV KALYALT CM CQLGLLQKPH VYEFASDIAP FLCHPNLWIR YGAVGFITVV ARQISTADVY CKLMPYLDPY ITQPIIQIER KLVLLSVL K EPVSRSIFDY ALRSKDITSL FRHLHMRQKK RNGSLPDCPP PEDPAIAQLL KKLLSQGMTE EEEDKLLALK DFMMKSNKA KANIVDQSHL HDSSQKGVID LAALGITGRQ VDLVKTKQEP DDKRARKHVK QDSNVNEEWK SMFGSLDPPN MPQALPKGSD QEVIQTGKP PRSESSAGIC VPLSTSSQVP EVTTVQNKKP VIPVLSSTIL PSTYQIRITT CKTELQQLIQ QKREQCNAER I AKQMMENA EWESKPPPPG WRPKGLLVAH LHEHKSAVNR IRVSDEHSLF ATCSNDGTVK IWNSQKMEGK TTTTRSILTY SR IGGRVKT LTFCQGSHYL AIASDNGAVQ LLGIEASKLP KSPKIHPLQS RILDQKEDGC VVDMHHFNSG AQSVLAYATV NGS LVGWDL RSSSNAWTLK HDLKSGLITS FAVDIHQCWL CIGTSSGTMA CWDMRFQLPI SSHCHPSRAR IRRLSMHPLY QSWV IAAVQ GNNEVSMWDM ETGDRRFTLW ASSAPPLSEL QPSPHSVHGI YCSPADGNPI LLTAGSDMKI RFWDLAYPER SYVVA GSTS SPSVSYYRKI IEGTEVVQEI QNKQKVGPSD DTPRRGPESL PVGHHDIITD VATFQTTQGF IVTASRDGIV KVWK

UniProtKB: Phosphoinositide 3-kinase regulatory subunit 4

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Macromolecule #2: Phosphatidylinositol 3-kinase catalytic subunit type 3

MacromoleculeName: Phosphatidylinositol 3-kinase catalytic subunit type 3
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphatidylinositol 3-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 101.680328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGEAEKFHYI YSCDLDINVQ LKIGSLEGKR EQKSYKAVLE DPMLKFSGLY QETCSDLYVT CQVFAEGKPL ALPVRTSYKA FSTRWNWNE WLKLPVKYPD LPRNAQVALT IWDVYGPGKA VPVGGTTVSL FGKYGMFRQG MHDLKVWPNV EADGSEPTKT P GRTSSTLS ...String:
MGEAEKFHYI YSCDLDINVQ LKIGSLEGKR EQKSYKAVLE DPMLKFSGLY QETCSDLYVT CQVFAEGKPL ALPVRTSYKA FSTRWNWNE WLKLPVKYPD LPRNAQVALT IWDVYGPGKA VPVGGTTVSL FGKYGMFRQG MHDLKVWPNV EADGSEPTKT P GRTSSTLS EDQMSRLAKL TKAHRQGHMV KVDWLDRLTF REIEMINESE KRSSNFMYLM VEFRCVKCDD KEYGIVYYEK DG DESSPIL TSFELVKVPD PQMSMENLVE SKHHKLARSL RSGPSDHDLK PNAATRDQLN IIVSYPPTKQ LTYEEQDLVW KFR YYLTNQ EKALTKFLKC VNWDLPQEAK QALELLGKWK PMDVEDSLEL LSSHYTNPTV RRYAVARLRQ ADDEDLLMYL LQLV QALKY ENFDDIKNGL EPTKKDSQSS VSENVSNSGI NSAEIDSSQI ITSPLPSVSS PPPASKTKEV PDGENLEQDL CTFLI SRAC KNSTLANYLY WYVIVECEDQ DTQQRDPKTH EMYLNVMRRF SQALLKGDKS VRVMRSLLAA QQTFVDRLVH LMKAVQ RES GNRKKKNERL QALLGDNEKM NLSDVELIPL PLEPQVKIRG IIPETATLFK SALMPAQLFF KTEDGGKYPV IFKHGDD LR QDQLILQIIS LMDKLLRKEN LDLKLTPYKV LATSTKHGFM QFIQSVPVAE VLDTEGSIQN FFRKYAPSEN GPNGISAE V MDTYVKSCAG YCVITYILGV GDRHLDNLLL TKTGKLFHID FGYILGRDPK PLPPPMKLNK EMVEGMGGTQ SEQYQEFRK QCYTAFLHLR RYSNLILNLF SLMVDANIPD IALEPDKTVK KVQDKFRLDL SDEEAVHYMQ SLIDESVHAL FAAVVEQIHK FAQYWRK

UniProtKB: Phosphatidylinositol 3-kinase catalytic subunit type 3

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Macromolecule #3: Beclin 1-associated autophagy-related key regulator

MacromoleculeName: Beclin 1-associated autophagy-related key regulator / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.387266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASPSGKGAR ALEAPGCGPR PLARDLVDSV DDAEGLYVAV ERCPLCNTTR RRLTCAKCVQ SGDFVYFDGR DRERFIDKKE RLSRLKSKQ EEFQKEVLKA MEGKWITDQL RWKIMSCKMR IEQLKQTICK GNEEMEKNSE GLLKTKEKNQ KLYSRAQRHQ E KKEKIQRH ...String:
MASPSGKGAR ALEAPGCGPR PLARDLVDSV DDAEGLYVAV ERCPLCNTTR RRLTCAKCVQ SGDFVYFDGR DRERFIDKKE RLSRLKSKQ EEFQKEVLKA MEGKWITDQL RWKIMSCKMR IEQLKQTICK GNEEMEKNSE GLLKTKEKNQ KLYSRAQRHQ E KKEKIQRH NRKLGDLVEK KTIDLRSHYE RLANLRRSHI LELTSVIFPI EEVKTGVRDP ADVSSESDSA MTSSTVSKLA EA RRTTYLS GRWVCDDHNG DTSISITGPW ISLPNNGDYS AYYSWVEEKK TTQGPDMEQS NPAYTISAAL CYATQLVNIL SHI LDVNLP KKLCNSEFCG ENLSKQKFTR AVKKLNANIL YLCFSQHVNL DQLQPLHTLR NLMYLVSPSS EHLGRSGPFE VRAD LEESM EFVDPGVAGE SDESGDERVS DEETDLGTDW ENLPSPRFCD IPSQSVEVSQ SQSTQASPPI ASSSAGGMIS SAAAS VTSW FKAYTGHR

UniProtKB: Beclin 1-associated autophagy-related key regulator

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Macromolecule #4: Beclin-1

MacromoleculeName: Beclin-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.953102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGSKTSNNS TMQVSFVCQR CSQPLKLDTS FKILDRVTIQ ELTAPLLTTA QAKPGETQEE ETNSGEEPFI ETPRQDGVSR RFIPPARMM STESANSFTL IGEASDGGTM ENLSRRLKVT GDLFDIMSGQ TDVDHPLCEE CTDTLLDQLD TQLNVTENEC Q NYKRCLEI ...String:
MEGSKTSNNS TMQVSFVCQR CSQPLKLDTS FKILDRVTIQ ELTAPLLTTA QAKPGETQEE ETNSGEEPFI ETPRQDGVSR RFIPPARMM STESANSFTL IGEASDGGTM ENLSRRLKVT GDLFDIMSGQ TDVDHPLCEE CTDTLLDQLD TQLNVTENEC Q NYKRCLEI LEQMNEDDSE QLQMELKELA LEEERLIQEL EDVEKNRKIV AENLEKVQAE AERLDQEEAQ YQREYSEFKR QQ LELDDEL KSVENQMRYA QTQLDKLKKT NVFNATFHIW HSGQFGTINN FRLGRLPSVP VEWNEINAAW GQTVLLLHAL ANK MGLKFQ RYRLVPYGNH SYLESLTDKS KELPLYCSGG LRFFWDNKFD HAMVAFLDCV QQFKEEVEKG ETRFCLPYRM DVEK GKIED TGGSGGSYSI KTQFNSEEQW TKALKFMLTN LKWGLAWVSS QFYNK

UniProtKB: Beclin-1

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Macromolecule #5: RB1-inducible coiled-coil protein 1

MacromoleculeName: RB1-inducible coiled-coil protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.325633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKLYVFLVNT GTTLTFDTEL TVQTVADLKH AIQSKYKIAI QHQVLVVNGG ECMAADRRVC TYSAGTDTNP IFLFNKEMIL CDRPPAIPK TTFSTENDME IKVEESLMMP AVFHTVASRT QLALEMYEVA KKLCSFCEGL VHDEHLQHQG WAAIMANLED C SNSYQKLL ...String:
MKLYVFLVNT GTTLTFDTEL TVQTVADLKH AIQSKYKIAI QHQVLVVNGG ECMAADRRVC TYSAGTDTNP IFLFNKEMIL CDRPPAIPK TTFSTENDME IKVEESLMMP AVFHTVASRT QLALEMYEVA KKLCSFCEGL VHDEHLQHQG WAAIMANLED C SNSYQKLL FKFESIYSNY LQSIEDIKLK LTHLGTAVSV MAKIPLLECL TRHSYRECLG RLDSLPEHED SEKAEMKRST EL VLSPDMP RTTNESLLTS FPKSVEHVSP DTADAESGKE IRESCQSTVH QQDETTIDTK DGDLPFFNVS LLDWINVQDR PND VESLVR KCFDSMSRLD PRIIRPFIAE CRQTIAKLDN QNMKAIKGLE DRLYALDQMI ASCGRLVNEQ KELAQGFLAN QKRA ENLKD ASVLPDLCLS HANQLMIMLQ NHRKLLDIKQ KCTTAKQELA NNLHVRLKWC CFVMLHADQD GEKLQALLRL VIELL ERVK IVEALSTVPQ MYCLAVVEVV RRKMFIKHYR EWAGALVKDG KRLYEAEKSK RESFGKLFRK SFLRNRLFRG LDSWPP SFC TQKPRKFDCE LPDISLKDLQ FLQSFCPSEV QPFLRVPLLC DFEPLHQHVL ALHNLVKAAQ SLDEMSQTIT DLLSEQK

UniProtKB: RB1-inducible coiled-coil protein 1

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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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
200.0 mMNaClNaCl
1.0 mMMgCl2MgCl2
10.0 mMC9H15O6PTCEP
4.0 mMC10H18N2O3d-Desthiobiotin
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: added 0.05% (w/v) octylglucopyranoside as surfactant.
DetailsThis sample was purified by strep pulldown.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4473551
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21937
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 21000 / Software - Name: cryoSPARC (ver. 4.3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9c82:
Structure of human ULK1C:PI3KC3-C1 supercomplex

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