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- EMDB-74527: Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Midd... -

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Basic information

Entry
Database: EMDB / ID: EMD-74527
TitleCryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus
Map dataSharpened consensus map
Sample
  • Complex: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus
    • Protein or peptide: Phosphoinositide 3-kinase regulatory subunit 4
    • Protein or peptide: Phosphatidylinositol 3-kinase catalytic subunit type 3
    • Protein or peptide: UV radiation resistance-associated gene protein
    • Protein or peptide: Beclin-1,Run domain Beclin-1-interacting and cysteine-rich domain-containing protein chimera
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
KeywordsLipid kinase / endocytic sorting / cytokinesis / autophagosome maturation / lysosome recycling / LC3-associated phagocytosis / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of autophagosome maturation / regulation of protein serine/threonine kinase activity / lytic vacuole / maintenance of Golgi location / phosphatidylinositol 3-kinase inhibitor activity / cellular response to aluminum ion / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / Synthesis of PIPs at the late endosome membrane ...negative regulation of autophagosome maturation / regulation of protein serine/threonine kinase activity / lytic vacuole / maintenance of Golgi location / phosphatidylinositol 3-kinase inhibitor activity / cellular response to aluminum ion / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / Synthesis of PIPs at the late endosome membrane / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / 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 / phosphatidylinositol phosphate binding / response to mitochondrial depolarisation / SARS-CoV-2 modulates autophagy / host-mediated activation of viral genome replication / presynaptic endosome / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / engulfment of apoptotic cell / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / positive regulation of autophagosome assembly / response to L-leucine / early endosome to late endosome transport / cytoplasmic side of mitochondrial outer membrane / negative regulation of autophagosome assembly / protein localization to phagophore assembly site / multivesicular body sorting pathway / receptor catabolic process / SMAD protein signal transduction / protein targeting to lysosome / late endosome to vacuole transport / negative regulation of endocytosis / endosome organization / pexophagy / double-strand break repair via classical nonhomologous end joining / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / positive regulation of autophagosome maturation / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / centrosome cycle / negative regulation of programmed cell death / phosphatidylinositol 3-kinase / spindle organization / 1-phosphatidylinositol-3-kinase activity / lysosome organization / response to vitamin E / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / Macroautophagy / phosphatidylinositol-mediated signaling / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / SNARE complex assembly / RSV-host interactions / p38MAPK cascade / phosphatidylinositol phosphate biosynthetic process / autolysosome / autophagosome membrane / PI3K Cascade / axoneme / chromosome, centromeric region / amyloid-beta metabolic process / autophagosome maturation / autophagosome assembly / RHO GTPases Activate NADPH Oxidases / immune system process / synaptic vesicle endocytosis / regulation of macroautophagy / phagocytosis / neuron development / cellular defense response / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / JNK cascade / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of autophagy / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of autophagy / autophagosome / cellular response to amino acid starvation / cellular response to copper ion / cellular response to epidermal growth factor stimulus / SNARE binding / regulation of cytokinesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / chromosome segregation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / trans-Golgi network
Similarity search - Function
: / : / Rubicon, PI3K-binding domain / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / : ...: / : / Rubicon, PI3K-binding domain / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / 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 / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / 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. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 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 / WD domain, G-beta repeat / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Protein kinase domain / WD40-repeat-containing domain superfamily / 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
Phosphoinositide 3-kinase regulatory subunit 4 / Beclin-1 / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Run domain Beclin-1-interacting and cysteine-rich domain-containing protein / UV radiation resistance-associated gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsChen M / Ni Q / Hurley JH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS134598 United States
Michael J. Fox FoundationASAP-000350 United States
CitationJournal: To Be Published
Title: Cryo-EM reconstruction of PI3KC3-C2 in complex with Rubicon Middle Region of C terminus
Authors: Chen M / Ni Q / Hurley JH
History
DepositionDec 16, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74527.png

Downloads & links

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Map

FileDownload / File: emd_74527.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 448 pix.
= 421.12 Å		0.94 Å/pix.
x 448 pix.
= 421.12 Å		0.94 Å/pix.
x 448 pix.
= 421.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.8103965 - 1.3788779
Average (Standard dev.)0.000139479 (±0.015837658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 421.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_74527_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_74527_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Phosphatidylinositol-3 kinase class III complex II in compl...

EntireName: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus
Components
  • Complex: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus
    • Protein or peptide: Phosphoinositide 3-kinase regulatory subunit 4
    • Protein or peptide: Phosphatidylinositol 3-kinase catalytic subunit type 3
    • Protein or peptide: UV radiation resistance-associated gene protein
    • Protein or peptide: Beclin-1,Run domain Beclin-1-interacting and cysteine-rich domain-containing protein chimera
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Human Phosphatidylinositol-3 kinase class III complex II in compl...

SupramoleculeName: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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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: 162.838141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFMPSSFSYS SWATCWLLCC LIILAKNSSI DGIEATMGNQ LAGIAPSQIL SVESYFSDIH DFEYDKSLGS TRFFKVARAK HREGLVVVK VFAIQDPTLP LTSYKQELEE LKIRLNSAQN CLPFQKASEK ASEKAAMLFR QYVRDNLYDR ISTRPFLNNI E KRWIAFQI ...String:
MFMPSSFSYS SWATCWLLCC LIILAKNSSI DGIEATMGNQ LAGIAPSQIL SVESYFSDIH DFEYDKSLGS TRFFKVARAK HREGLVVVK VFAIQDPTLP LTSYKQELEE LKIRLNSAQN CLPFQKASEK ASEKAAMLFR QYVRDNLYDR ISTRPFLNNI E KRWIAFQI LTAVDQAHKS GVRHGDIKTE NVMVTSWNWV LLTDFASFKP TYLPEDNPAD FNYFFDTSRR RTCYIAPERF VD GGMFATE LEYMRDPSTP LVDLNSNQRR RGELKRAMDI FSAGCVIAEL FTEGVPLFDL SQLLAYRNGH FFPEQVLNKI EDH SIRELV TQMIHREPDK RLEAEDYLKQ QRGNAFPEIF YTFLQPYMAQ FAKETFLSAD ERILVIRKDL GNIIHNLCGH DLPE KAEGE PKENGLVILV SVITSCLQTL KYCDSKLAAL ELILHLAPRL SVEILLDRIT PYLLHFSNDS VPRVRAEALR TLTKV LALV KEVPRNDINI YPEYILPGIA HLAQDDATIV RLAYAENIAL LAETALRFLE LVQLKNLNME NDPNNEEIDE VTHPNG NYD TELQALHEMV QQKVVTLLSD PENIVKQTLM ENGITRLCVF FGRQKANDVL LSHMITFLND KNDWHLRGAF FDSIVGV AA YVGWQSSSIL KPLLQQGLSD AEEFVIVKAL YALTCMCQLG LLQKPHVYEF ASDIAPFLCH PNLWIRYGAV GFITVVAR Q ISTADVYCKL MPYLDPYITQ PIIQIERKLV LLSVLKEPVS RSIFDYALRS KDITSLFRHL HMRQKKRNGS LPDCPPPED PAIAQLLKKL LSQGMTEEEE DKLLALKDFM MKSNKAKANI VDQSHLHDSS QKGVIDLAAL GITGRQVDLV KTKQEPDDKR ARKHVKQDS NVNEEWKSMF GSLDPPNMPQ ALPKGSDQEV IQTGKPPRSE SSAGICVPLS TSSQVPEVTT VQNKKPVIPV L SSTILPST YQIRITTCKT ELQQLIQQKR EQCNAERIAK QMMENAEWES KPPPPGWRPK GLLVAHLHEH KSAVNRIRVS DE HSLFATC SNDGTVKIWN SQKMEGKTTT TRSILTYSRI GGRVKTLTFC QGSHYLAIAS DNGAVQLLGI EASKLPKSPK IHP LQSRIL DQKEDGCVVD MHHFNSGAQS VLAYATVNGS LVGWDLRSSS NAWTLKHDLK SGLITSFAVD IHQCWLCIGT SSGT MACWD MRFQLPISSH CHPSRARIRR LSMHPLYQSW VIAAVQGNNE VSMWDMETGD RRFTLWASSA PPLSELQPSP HSVHG IYCS PADGNPILLT AGSDMKIRFW DLAYPERSYV VAGSTSSPSV SYYRKIIEGT EVVQEIQNKQ KVGPSDDTPR RGPESL PVG HHDIITDVAT FQTTQGFIVT ASRDGIVKVW KGTENLYFQS GMAAWSHPQF EKGGGARGGS GGGSWSHPQF EKGFDYK DD DDK

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: UV radiation resistance-associated gene protein

MacromoleculeName: UV radiation resistance-associated gene protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.258836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSASASVGGP VPQPPPGPAA ALPPGSAARA LHVELPSQQR RLRHLRNIAA RNIVNRNGHQ LLDTYFTLHL CSTEKIYKEF YRSEVIKNS LNPTWRSLDF GIMPDRLDTS VSCFVVKIWG GKENIYQLLI EWKVCLDGLK YLGQQIHARN QNEIIFGLND G YYGAPFEH ...String:
MSASASVGGP VPQPPPGPAA ALPPGSAARA LHVELPSQQR RLRHLRNIAA RNIVNRNGHQ LLDTYFTLHL CSTEKIYKEF YRSEVIKNS LNPTWRSLDF GIMPDRLDTS VSCFVVKIWG GKENIYQLLI EWKVCLDGLK YLGQQIHARN QNEIIFGLND G YYGAPFEH KGYSNAQKTI LLQVDQNCVR NSYDVFSLLR LHRAQCAIKQ TQVTVQKIGK EIEEKLRLTS TSNELKKKSE CL QLKILVL QNELERQKKA LGREVALLHK QQIALQDKGS AFSAEHLKLQ LQKESLNELR KECTAKRELF LKTNAQLTIR CRQ LLSELS YIYPIDLNEH KDYFVCGVKL PNSEDFQAKD DGSIAVALGY TAHLVSMISF FLQVPLRYPI IHKGSRSTIK DNIN DKLTE KEREFPLYPK GGEKLQFDYG VYLLNKNIAQ LRYQHGLGTP DLRQTLPNLK NFMEHGLMVR CDRHHTSSAI PVPKR QSSI FGGADVGFSG GIPSPDKGHR KRASSENERL QYKTPPPSYN SALAQPVTTV PSMGETERKI TSLSSSLDTS LDFSKE NKK KGEDLVGSLN GGHANVHPSQ EQGEALSGHR ATVNGTLLPS EQAGSASVQL PGEFHPVSEA ELCCTVEQAE EIIGLEA TG FASGDQLEAF NCIPVDSAVA VECDEQVLGE FEEFSRRIYA LNENVSSFRR PRRSSDK

UniProtKB: UV radiation resistance-associated gene protein

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Macromolecule #4: Beclin-1,Run domain Beclin-1-interacting and cysteine-rich domain...

MacromoleculeName: Beclin-1,Run domain Beclin-1-interacting and cysteine-rich domain-containing protein chimera
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.300797 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 QFYNKGGSGG SGGSGGSQSL ISYLSEQDFG SCADL EKEN AHFSISESLI AAIELMKCNM MSQCLEEEEV EEEDSDREIQ ELKQKIRLRR QQIRTKNLLP MYQEAEHGSF RVTSSS SQF SSRDSAQLSD SGSADEVDEF EIQDADIRRN TASSSKSFVS SQSFSHCFLH STSAEAVAMG LLKQFEGMQL PAASELE WL VPEHDAPQKL LPIPDSLPIS P

UniProtKB: Beclin-1, Run domain Beclin-1-interacting and cysteine-rich domain-containing protein

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloride
2.0 mMMgCl2Magnesium chloride
25.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMTris(2-carboxyethyl)phosphine
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold prediction model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 175726
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.5.3)
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 / Overall B value: 95.23
Output model

PDB-9zpd:
Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus

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