[English] 日本語
Yorodumi
- EMDB-40738: Structure of human ULK1C:PI3KC3-C1 supercomplex -

+
Open data


ID or keywords:

Loading...

-
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 / Toll Like Receptor 9 (TLR9) Cascade / omegasome membrane / protein lipidation / regulation of protein lipidation ...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 / omegasome membrane / protein lipidation / regulation of protein lipidation / Synthesis of PIPs at the late endosome membrane / neuron projection regeneration / ribophagy / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / glycophagy / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / mitochondria-associated endoplasmic reticulum membrane contact site / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / engulfment of apoptotic cell / nucleophagy / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / regulation of protein complex stability / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / phagophore assembly site membrane / suppression by virus of host autophagy / protein targeting to lysosome / protein targeting to vacuole / early endosome to late endosome transport / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / late endosome to vacuole transport / SMAD protein signal transduction / RAB GEFs exchange GTP for GDP on RABs / protein kinase regulator activity / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / axon extension / negative regulation of programmed cell death / response to iron(II) ion / TBC/RABGAPs / reticulophagy / positive regulation of protein targeting to mitochondrion / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / post-transcriptional regulation of gene expression / mitotic metaphase chromosome alignment / Macroautophagy / 1-phosphatidylinositol-3-kinase activity / autophagosome membrane docking / Receptor Mediated Mitophagy / RSV-host interactions / lysosome organization / endosome to lysosome transport / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / response to starvation / p38MAPK cascade / axoneme / autophagosome membrane / cellular response to nutrient levels / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / mitophagy / autophagosome maturation / positive regulation of cell size / autophagosome assembly / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / response to vitamin E / negative regulation of reactive oxygen species metabolic process / autophagosome / neuron development / regulation of macroautophagy / amyloid-beta metabolic process / negative regulation of protein-containing complex assembly / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / JNK cascade / phagocytic vesicle
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 / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Serine/threonine-protein kinase, Ulk1/Ulk2 / : / ATG1-like, MIT domain 2 / Beclin-1, BH3 domain ...UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Serine/threonine-protein kinase, Ulk1/Ulk2 / : / ATG1-like, MIT domain 2 / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / 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 / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40738.png

Downloads & links

-
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
Voxel sizeX=Y=Z: 1.115 Å
Density
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 °

-
Supplemental data

-
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)

-
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)

-
Sample components

+
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

+
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

+
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)

+
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)

+
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

+
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

+
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

+
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

+
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

+
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

+
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium chloridesodium 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

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 968884
Startup modelType of model: INSILICO MODEL
Initial 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)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
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

-
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-8srq:
Structure of human ULK1C:PI3KC3-C1 supercomplex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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

-
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

Read more