[English] 日本語
Yorodumi
- EMDB-17790: Structure of tissue-specific lipid scramblase ATG9B homotrimer, r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17790
TitleStructure of tissue-specific lipid scramblase ATG9B homotrimer, refined without imposing symmetry
Map dataATG9B C1 map
Sample
  • Complex: Homotrimer of ATG9B
    • Protein or peptide: Autophagy-related protein 9B
Keywordsmembrane protein / lipid scramblase / autophagy / phagopore / lipid transporter / Atg9 / Atg9B / LIPID TRANSPORT
Function / homology
Function and homology information


phospholipid scramblase activity / programmed necrotic cell death / nucleophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / phagophore assembly site / bone morphogenesis / Macroautophagy / autophagosome assembly / autophagosome ...phospholipid scramblase activity / programmed necrotic cell death / nucleophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / phagophore assembly site / bone morphogenesis / Macroautophagy / autophagosome assembly / autophagosome / trans-Golgi network / recycling endosome membrane / Golgi membrane / endoplasmic reticulum membrane
Similarity search - Function
Autophagy-related protein 9 / Autophagy protein ATG9
Similarity search - Domain/homology
Autophagy-related protein 9B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsChiduza GN / Pye VE / Tooze SA / Cherepanov P
Funding support United Kingdom, European Union, 5 items
OrganizationGrant numberCountry
Cancer Research UKCC2134, CC2058 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2134, CC2058 United Kingdom
Wellcome TrustCC2134, CC2058 United Kingdom
European Research Council (ERC)788708European Union
The Francis Crick InstituteCC2134, CC2058 United Kingdom
CitationJournal: Autophagy / Year: 2024
Title: ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A.
Authors: George N Chiduza / Acely Garza-Garcia / Eugenia Almacellas / Stefano De Tito / Valerie E Pye / Alexander R van Vliet / Peter Cherepanov / Sharon A Tooze /
Abstract: Macroautophagy/autophagy is a fundamental aspect of eukaryotic biology, and the autophay-related protein ATG9A is part of the core machinery facilitating this process. In addition to ATG9A ...Macroautophagy/autophagy is a fundamental aspect of eukaryotic biology, and the autophay-related protein ATG9A is part of the core machinery facilitating this process. In addition to ATG9A vertebrates encode ATG9B, a poorly characterized paralog expressed in a subset of tissues. Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein. Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. By establishing the molecular structure and function of ATG9B, our results inform the exploration of niche roles for autophagy machinery in more complex eukaryotes and reveal insights relevant across species. ATG: autophagy related; CHS: cholesteryl hemisuccinate; cryo-EM: single-particle cryogenic electron microscopy; CTF: contrast transfer function: CTH: C- terminal α helix; FSC: fourier shell correlation; HDIR: HORMA domain interacting region; LMNG: lauryl maltose neopentyl glycol; MD: molecular dynamics simulations; MSA: multiple sequence alignment; NBD-PE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl ammonium salt); POPC: palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; RBG: repeating beta groove domain; RMSD: root mean square deviation; SEC: size-exclusion chromatography; TMH: transmembrane helix.
History
DepositionJul 4, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17790.png

Downloads & links

-
Map

FileDownload / File: emd_17790.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATG9B C1 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.377
Minimum - Maximum-2.2974653 - 2.6684382
Average (Standard dev.)0.0038149243 (±0.062386777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_17790_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: ATG9B C1 DeepEMhancer map

Fileemd_17790_additional_1.map
AnnotationATG9B C1 DeepEMhancer map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: ATG9B C1 half map 1

Fileemd_17790_half_map_1.map
AnnotationATG9B C1 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: ATG9B C1 half map 2

Fileemd_17790_half_map_2.map
AnnotationATG9B C1 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homotrimer of ATG9B

EntireName: Homotrimer of ATG9B
Components
  • Complex: Homotrimer of ATG9B
    • Protein or peptide: Autophagy-related protein 9B

-
Supramolecule #1: Homotrimer of ATG9B

SupramoleculeName: Homotrimer of ATG9B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 303 KDa

-
Macromolecule #1: Autophagy-related protein 9B

MacromoleculeName: Autophagy-related protein 9B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKDY KDDDDKDYKD DDDKHHHHHH ENLYFQMVSR MGWGGRRRRL GRWGDLGPGS VPLLPMPLPP PPPPSCRGPG GGRISIFSLS PAPHTR SSP SSFSPPTAGP PCSVLQGTGA SQSCHSALPI PATPPTQAQP AMTPASASPS WGSHSTP PL APATPTPSQQ ...String:
DYKDDDDKDY KDDDDKDYKD DDDKHHHHHH ENLYFQMVSR MGWGGRRRRL GRWGDLGPGS VPLLPMPLPP PPPPSCRGPG GGRISIFSLS PAPHTR SSP SSFSPPTAGP PCSVLQGTGA SQSCHSALPI PATPPTQAQP AMTPASASPS WGSHSTP PL APATPTPSQQ CPQDSPGLRV GPLIPEQDYE RLEDCDPEGS QDSPIHGEEQ QPLLHVPE G LRGSWHHIQN LDSFFTKIYS YHQRNGFACI LLEDVFQLGQ FIFIVTFTTF LLRCVDYNV LFANQPSNHT RPGPFHSKVT LSDAILPSAQ CAERIRSSPL LVLLLVLAAG FWLVQLLRSV CNLFSYWDI QVFYREALHI PPEELSSVPW AEVQSRLLAL QRSGGLCVQP RPLTELDIHH R ILRYTNYQ VALANKGLLP ARCPLPWGGS AAFLSRGLAL NVDLLLFRGP FSLFRGGWEL PH AYKRSDQ RGALAARWGR TVLLLAALNL ALSPLVLAWQ VLHVFYSHVE LLRREPGALG ARG WSRLAR LQLRHFNELP HELRARLARA YRPAAAFLRT AAPPAPLRTL LARQLVFFAG ALFA ALLVL TVYDEDVLAV EHVLTAMTAL GVTATVARSF IPEEQCQGRA PQLLLQTALA HMHYL PEEP GPGGRDRAYR QMAQLLQYRA VSLLEELLSP LLTPLFLLFW FRPRALEIID FFHHFT VDV AGVGDICSFA LMDVKRHGHP QWLSAGQTEA SLSQRAEDGK TELSLMRFSL AHPLWRP PG HSSKFLGHLW GRVQQDAAAW GATSARGPST PGVLSNCTSP LPEAFLANLF VHPLLPPR D LSPTAPCPAA ATASLLASIS RIAQDPSSVS PGGTGGQKLA QLPELASAEM SLHVIYLHQ LHQQQQQQEP WGEAAASILS RPCSSPSQPP SPDEEKPSWS SDGSSPASSP RQQWGTQKAR NLFPGGFQV TTDTQKEPDR ASCTD

UniProtKB: Autophagy-related protein 9B

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 8.5
Details: 20 mM Tris-HCl, pH 8.5; 200 mM NaCl; 1 mM TCEP; 10% glycerol supplemented with 0.001% w/v lauryl maltose neopentyl glycol and 0.0002% w/v cholesteryl hemisuccinate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 46296 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 37217 / Average exposure time: 1.2 sec. / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 6818472
Startup modelType of model: NONE
Details: Generated ab initio from selected 2D classes using cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 104050
FSC plot (resolution estimation)

+
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