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- EMDB-40738: Structure of human ULK1C:PI3KC3-C1 supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-40738
TitleStructure of human ULK1C:PI3KC3-C1 supercomplex
Map dataz-flipped from the original map
Sample
  • Complex: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex
    • Complex: Human autophagy initiation ULK1 complex core
      • Protein or peptide: RB1-inducible coiled-coil protein 1
      • Protein or peptide: Serine/threonine-protein kinase ULK1
      • Protein or peptide: Autophagy-related protein 13
    • Complex: Human autophagy initiation 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-C 35 kDa
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 / neuron projection regeneration / positive regulation of protein lipidation / omegasome membrane / postsynaptic endosome ...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 / neuron projection regeneration / positive regulation of protein lipidation / omegasome membrane / 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 / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / ribophagy / host-mediated activation of viral genome replication / response to mitochondrial depolarisation / glycophagy / presynaptic endosome / positive regulation of attachment of mitotic spindle microtubules to kinetochore / mitochondria-associated endoplasmic reticulum membrane contact site / negative regulation of lysosome organization / engulfment of apoptotic cell / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / regulation of protein complex stability / positive regulation of autophagosome assembly / early endosome to late endosome transport / response to L-leucine / cytoplasmic side of mitochondrial outer membrane / negative regulation of autophagosome assembly / protein localization to phagophore assembly site / phosphatidylinositol 3-kinase regulator activity / receptor catabolic process / phagophore assembly site membrane / protein targeting to vacuole / protein targeting to lysosome / SMAD protein signal transduction / late endosome to vacuole transport / endosome organization / pexophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / protein kinase regulator activity / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / axon extension / TBC/RABGAPs / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / reticulophagy / negative regulation of programmed cell death / positive regulation of protein targeting to mitochondrion / phosphatidylinositol 3-kinase / lysosome organization / 1-phosphatidylinositol-3-kinase activity / post-transcriptional regulation of gene expression / response to vitamin E / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / Receptor Mediated Mitophagy / response to starvation / endosome to lysosome transport / cellular response to stress / Macroautophagy / phosphatidylinositol-mediated signaling / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / autophagosome membrane docking / RSV-host interactions / p38MAPK cascade / phosphatidylinositol phosphate biosynthetic process / negative regulation of protein phosphorylation / autolysosome / autophagosome membrane / PI3K Cascade / axoneme / autophagosome assembly / autophagosome maturation / amyloid-beta metabolic process / RHO GTPases Activate NADPH Oxidases / positive regulation of cell size / synaptic vesicle endocytosis / regulation of macroautophagy / neuron development / cellular defense response / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway
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 / Serine/threonine-protein kinase, Ulk1/Ulk2 / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Autophagy-related protein 13 ...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 / Serine/threonine-protein kinase, Ulk1/Ulk2 / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / 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 / HORMA domain superfamily / 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 / WD domain, G-beta repeat / Armadillo-type fold / Trp-Asp (WD) repeats signature. / 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 13 / Serine/threonine-protein kinase ULK1 / 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: 6.2 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
CitationJournal: 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
DepositionMay 5, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40738.png

Downloads & links

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Map

FileDownload / File: emd_40738.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationz-flipped from the original map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 600 pix.
= 669. Å		1.12 Å/pix.
x 600 pix.
= 669. Å		1.12 Å/pix.
x 600 pix.
= 669. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.115 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.75742245 - 1.3113143
Average (Standard dev.)-0.00013459552 (±0.027993353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 669.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_40738_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_40738_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
    • Complex: Human autophagy initiation ULK1 complex core
      • Protein or peptide: RB1-inducible coiled-coil protein 1
      • Protein or peptide: Serine/threonine-protein kinase ULK1
      • Protein or peptide: Autophagy-related protein 13
    • Complex: Human autophagy initiation 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-C 35 kDa

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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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 362 KDa

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Supramolecule #2: Human autophagy initiation ULK1 complex core

SupramoleculeName: Human autophagy initiation ULK1 complex core / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human autophagy initiation PI3KC3-C1 complex

SupramoleculeName: Human autophagy initiation PI3KC3-C1 complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#7
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: RB1-inducible coiled-coil protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.808477 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 QPFLRVP

UniProtKB: RB1-inducible coiled-coil protein 1

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Macromolecule #2: Serine/threonine-protein kinase ULK1

MacromoleculeName: Serine/threonine-protein kinase ULK1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.113896 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HTEILRGLRF TLLFVQHVLE IAALKGSASE AAGGPEYQLQ ESVVADQISL LSREWGFAEQ LVLYLKVAEL LSSGLQSAID QIRAGKLCL SSTVKQVVRR LNELYKASVV SCQGLSLRLQ RFFLDKQRLL DRIHSITAER LIFSHAVQMV QSAALDEMFQ H REGCVPRY ...String:
HTEILRGLRF TLLFVQHVLE IAALKGSASE AAGGPEYQLQ ESVVADQISL LSREWGFAEQ LVLYLKVAEL LSSGLQSAID QIRAGKLCL SSTVKQVVRR LNELYKASVV SCQGLSLRLQ RFFLDKQRLL DRIHSITAER LIFSHAVQMV QSAALDEMFQ H REGCVPRY HKALLLLEGL QHMLSDQADI ENVTKCKLCI ERRLSAL

UniProtKB: Serine/threonine-protein kinase ULK1

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Macromolecule #3: Autophagy-related protein 13

MacromoleculeName: Autophagy-related protein 13 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.805392 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DLGTFYREFQ NPPQLSSLSI DIGAQSMAED LDSLPEKLAV HEKNVREFDA FVETLQGSDE A

UniProtKB: Autophagy-related protein 13

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Macromolecule #4: Phosphoinositide 3-kinase regulatory subunit 4

MacromoleculeName: Phosphoinositide 3-kinase regulatory subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 151.899203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SVESYFSDIH DFEYDKSLGS TRFFKVARAK HREGLVVVKV FAIQDPTLPL TSYKQELEEL KIRLNSAQNC LPFQKASEKA SEKAAMLFR QYVRDNLYDR ISTRPFLNNI EKRWIAFQIL TAVDQAHKSG VRHGDIKTEN VMVTSWNWVL LTDFASFKPT Y LPEDNPAD ...String:
SVESYFSDIH DFEYDKSLGS TRFFKVARAK HREGLVVVKV FAIQDPTLPL TSYKQELEEL KIRLNSAQNC LPFQKASEKA SEKAAMLFR QYVRDNLYDR ISTRPFLNNI EKRWIAFQIL TAVDQAHKSG VRHGDIKTEN VMVTSWNWVL LTDFASFKPT Y LPEDNPAD FNYFFDTSRR RTCYIAPERF VDGGMFATEL EYMRDPSTPL VDLNSNQRTR GELKRAMDIF SAGCVIAELF TE GVPLFDL SQLLAYRNGH FFPEQVLNKI EDHSIRELVT QMIHREPDKR LEAEDYLKQQ RGNAFPEIFY TFLQPYMAQF AKE TFLSAD ERILVIRKDL GNIIHNLCGH DLPEKAEGEP KENGLVILVS VITSCLQTLK YCDSKLAALE LILHLAPRLS VEIL LDRIT PYLLHFSNDS VPRVRAEALR TLTKVLALVK EVPRNDINIY PEYILPGIAH LAQDDATIVR LAYAENIALL AETAL RFLE LVQLKNLNME NDPNNEEIDE VTHPNGNYDT ELQALHEMVQ QKVVTLLSDP ENIVKQTLME NGITRLCVFF GRQKAN DVL LSHMITFLND KNDWHLRGAF FDSIVGVAAY VGWQSSSILK PLLQQGLSDA EEFVIVKALY ALTCMCQLGL LQKPHVY EF ASDIAPFLCH PNLWIRYGAV GFITVVARQI STADVYCKLM PYLDPYITQP IIQIERKLVL LSVLKEPVSR SIFDYALR S KDITSLFRHL HMRQKKRNGS LPDCPPPEDP AIAQLLKKLL SQGMTEEEED KLLALKDFMM KSNKAKANIV DQSHLHDSS QKGVIDLAAL GITGRQVDLV KTKQEPDDKR ARKHVKQDSN VNEEWKSMFG SLDPPNMPQA LPKGSDQEVI QTGKPPRSES SAGICVPLS TSSQVPEVTT VQNKKPVIPV LSSTILPSTY QIRITTCKTE LQQLIQQKRE QCNAERIAKQ MMENAEWESK P PPPGWRPK GLLVAHLHEH KSAVNRIRVS DEHSLFATCS NDGTVKIWNS QKMEGKTTTT RSILTYSRIG GRVKTLTFCQ GS HYLAIAS DNGAVQLLGI EASKLPKSPK IHPLQSRILD QKEDGCVVDM HHFNSGAQSV LAYATVNGSL VGWDLRSSSN AWT LKHDLK SGLITSFAVD IHQCWLCIGT SSGTMACWDM RFQLPISSHC HPSRARIRRL SMHPLYQSWV IAAVQGNNEV SMWD METGD RRFTLWASSA PPLSELQPSP HSVHGIYCSP ADGNPILLTA GSDMKIRFWD LAYPERSYVV AGSTSSPSVS YYRKI IEGT EVVQEIQNKQ KVGPSDDTPR RGPESLPVGH HDIITDVATF QTTQGFIVTA SRDGIVKVWK

UniProtKB: Phosphoinositide 3-kinase regulatory subunit 4

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Macromolecule #5: Phosphatidylinositol 3-kinase catalytic subunit type 3

MacromoleculeName: Phosphatidylinositol 3-kinase catalytic subunit type 3
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphatidylinositol 3-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.533104 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEKFHYIYSC DLDINVQLKI GSLEGKREQK SYKAVLEDPM LKFSGLYQET CSDLYVTCQV FAEGKPLALP VRTSYKAFST RWNWNEWLK LPVKYPDLPR NAQVALTIWD VYGPGKAVPV GGTTVSLFGK YGMFRQGMHD LKVWPNVEAD GSEPTKTPGR T SSTLSEDQ ...String:
AEKFHYIYSC DLDINVQLKI GSLEGKREQK SYKAVLEDPM LKFSGLYQET CSDLYVTCQV FAEGKPLALP VRTSYKAFST RWNWNEWLK LPVKYPDLPR NAQVALTIWD VYGPGKAVPV GGTTVSLFGK YGMFRQGMHD LKVWPNVEAD GSEPTKTPGR T SSTLSEDQ MSRLAKLTKA HRQGHMVKVD WLDRLTFREI EMINESEKRS SNFMYLMVEF RCVKCDDKEY GIVYYEKDGD ES SPILTSF ELVKVPDPQM SMENLVESKH HKLARSL

UniProtKB: Phosphatidylinositol 3-kinase catalytic subunit type 3

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Macromolecule #6: Beclin 1-associated autophagy-related key regulator

MacromoleculeName: Beclin 1-associated autophagy-related key regulator / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.824039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ERLSRLKSKQ EEFQKEVLKA MEGKWITDQL RWKIMSCKMR IEQLKQTICK GNEEMEKNSE GLLKTKEKNQ KLYSRAQRHQ EKKEKIQRH NRKLGDLVEK KTIDLRSHYE RLANLRRSHI LELTSVIFPI EEVKTGVRDP ADVSSESDSA MTSSTVSKLA E ARRTTYLS ...String:
ERLSRLKSKQ EEFQKEVLKA MEGKWITDQL RWKIMSCKMR IEQLKQTICK GNEEMEKNSE GLLKTKEKNQ KLYSRAQRHQ EKKEKIQRH NRKLGDLVEK KTIDLRSHYE RLANLRRSHI LELTSVIFPI EEVKTGVRDP ADVSSESDSA MTSSTVSKLA E ARRTTYLS GRWVCDDHNG DTSISITGPW ISLPNNGDYS AYYSWVEEKK TTQGPDMEQS NPAYTISAAL CYATQLVNIL SH ILDVNLP KKLCNSEFCG ENLSKQKFTR AVKKLNANIL YLCFSQHVNL DQLQPLHTLR NLMYLVSPSS EHLGRSGPFE VR

UniProtKB: Beclin 1-associated autophagy-related key regulator

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Macromolecule #7: Beclin-1-C 35 kDa

MacromoleculeName: Beclin-1-C 35 kDa / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.504809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DTQLNVTENE CQNYKRCLEI LEQMNEDDSE QLQMELKELA LEEERLIQEL EDVEKNRKIV AENLEKVQAE AERLDQEEAQ YQREYSEFK RQQLELDDEL KSVENQMRYA QTQLDKLKKT NVFNATFHIW HSGQFGTINN FRLGRLPSVP VEWNEINAAW G QTVLLLHA ...String:
DTQLNVTENE CQNYKRCLEI LEQMNEDDSE QLQMELKELA LEEERLIQEL EDVEKNRKIV AENLEKVQAE AERLDQEEAQ YQREYSEFK RQQLELDDEL KSVENQMRYA QTQLDKLKKT NVFNATFHIW HSGQFGTINN FRLGRLPSVP VEWNEINAAW G QTVLLLHA LANKMGLKFQ RYRLVPYGNH SYLESLTDKS KELPLYCSGG LRFFWDNKFD HAMVAFLDCV QQFKEEVEKG ET RFCLPYR MDVEKGKIED TGGSGGSYSI KTQFNSEEQW TKALKFMLTN LKWGLAWVSS QFYN

UniProtKB: Beclin-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

Concentration0.35 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
25.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / 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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3421 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination 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: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 968884
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 42315
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 3D classificationNumber classes: 3 / Avg.num./class: 42315 / Software - Name: cryoSPARC (ver. 4.1.1)

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Atomic model buiding 1

Initial model
PDB IDChain

8soi

source_name: PDB, initial_model_type: experimental model

8sor

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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