[English] 日本語
Yorodumi
- EMDB-40715: Structure of human ULK1 complex core (2:2:2 stoichiometry) in the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40715
TitleStructure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture
Map data
Sample
  • 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
KeywordsAutophagy / Protein kinase / Complex / IMMUNE SYSTEM
Function / homology
Function and homology information


omegasome membrane / regulation of protein lipidation / glycophagy / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / nucleophagy / protein localization to phagophore assembly site ...omegasome membrane / regulation of protein lipidation / glycophagy / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / nucleophagy / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / reticulophagy / TBC/RABGAPs / positive regulation of protein targeting to mitochondrion / Macroautophagy / Receptor Mediated Mitophagy / response to starvation / autophagosome membrane / cellular response to nutrient levels / mitophagy / autophagosome assembly / positive regulation of cell size / autophagosome / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of autophagy / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / protein serine/threonine kinase activator activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / Regulation of TNFR1 signaling / macroautophagy / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / protein localization / recycling endosome / small GTPase binding / autophagy / neuron projection development / GTPase binding / heart development / peptidyl-serine phosphorylation / nuclear membrane / mitochondrial outer membrane / protein autophosphorylation / lysosome / molecular adaptor activity / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / cell cycle / axon / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / signal transduction / mitochondrion / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / Autophagy-related protein 13, N-terminal ...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 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / HORMA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.85 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 4, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40715.png

Downloads & links

-
Map

FileDownload / File: emd_40715.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.5738211 - 1.4306266
Average (Standard dev.)-0.00036695247 (±0.02461333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A

Fileemd_40715_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_40715_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human autophagy initiation ULK1 complex core

EntireName: Human autophagy initiation ULK1 complex core
Components
  • 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

-
Supramolecule #1: Human autophagy initiation ULK1 complex core

SupramoleculeName: Human autophagy initiation ULK1 complex core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 230 KDa

-
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: 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

-
Macromolecule #2: Serine/threonine-protein kinase ULK1

MacromoleculeName: Serine/threonine-protein kinase ULK1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.190145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQEHTEILR GLRFTLLFVQ HVLEIAALKG SASEAAGGPE YQLQESVVAD QISLLSREWG FAEQLVLYLK VAELLSSGLQ SAIDQIRAG KLCLSSTVKQ VVRRLNELYK ASVVSCQGLS LRLQRFFLDK QRLLDRIHSI TAERLIFSHA VQMVQSAALD E MFQHREGC ...String:
MEQEHTEILR GLRFTLLFVQ HVLEIAALKG SASEAAGGPE YQLQESVVAD QISLLSREWG FAEQLVLYLK VAELLSSGLQ SAIDQIRAG KLCLSSTVKQ VVRRLNELYK ASVVSCQGLS LRLQRFFLDK QRLLDRIHSI TAERLIFSHA VQMVQSAALD E MFQHREGC VPRYHKALLL LEGLQHMLSD QADIENVTKC KLCIERRLSA LLTGICA

-
Macromolecule #3: Autophagy-related protein 13

MacromoleculeName: Autophagy-related protein 13 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.096969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
HDVLETIFVR KVGAFVNKPI NQVTLTSLDI PFAMFAPKNL ELEDTDPMVN PPDSPETESP LQGSLHSDGS SGGSSGNTHD DFVMIDFKP AFSKDDILPM DLGTFYREFQ NPPQLSSLSI DIGAQSMAED LDSLPEKLAV HEKNVREFDA FVETLQ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
300.0 mMNaClSodium chloridesodium chloride
25.0 mMC9H15O6PTCEP
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

-
Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 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: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5383 / Average electron dose: 50.0 e/Å2

-
Image processing

Particle selectionNumber selected: 97987
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 97987 / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 97987

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8sqz:
Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture

+
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