[English] 日本語
Yorodumi
- PDB-7yo8: Crystal structure of fission yeast Hfl1 LIR fused to human GABARAPL2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yo8
TitleCrystal structure of fission yeast Hfl1 LIR fused to human GABARAPL2
ComponentsTransmembrane protein 184 homolog C30D11.06c,Gamma-aminobutyric acid receptor-associated protein-like 2
KeywordsPROTEIN TRANSPORT / Autophagy / Vacuole / Autophagosome
Function / homology
Function and homology information


negative regulation of proteasomal protein catabolic process / protein localization to endoplasmic reticulum / intra-Golgi vesicle-mediated transport / vacuole organization / GABA receptor binding / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / fungal-type vacuole membrane / TBC/RABGAPs / cellular response to nitrogen starvation ...negative regulation of proteasomal protein catabolic process / protein localization to endoplasmic reticulum / intra-Golgi vesicle-mediated transport / vacuole organization / GABA receptor binding / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / fungal-type vacuole membrane / TBC/RABGAPs / cellular response to nitrogen starvation / Macroautophagy / beta-tubulin binding / autophagosome membrane / transmembrane transporter activity / autophagosome assembly / autophagosome maturation / mitophagy / autophagosome / SNARE binding / autophagy / protein transport / ATPase binding / microtubule binding / cytoplasmic vesicle / Golgi membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / Golgi apparatus / membrane / cytosol / cytoplasm
Similarity search - Function
Organic solute transporter subunit alpha/Transmembrane protein 184 / Organic solute transporter Ostalpha / Organic solute transporter Ostalpha / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein-like 2 / Vacuole membrane protein hfl11
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsYamasaki, A. / Noda, N.N.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03989 Japan
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Society for the Promotion of Science (JSPS)17K18339 Japan
Japan Science and TechnologyJPMJCR20E3 Japan
CitationJournal: Autophagy / Year: 2023
Title: Development of new tools to study membrane-anchored mammalian Atg8 proteins.
Authors: Park, S.W. / Jeon, P. / Yamasaki, A. / Lee, H.E. / Choi, H. / Mun, J.Y. / Jun, Y.W. / Park, J.H. / Lee, S.H. / Lee, S.K. / Lee, Y.K. / Song, H.K. / Lazarou, M. / Cho, D.H. / Komatsu, M. / ...Authors: Park, S.W. / Jeon, P. / Yamasaki, A. / Lee, H.E. / Choi, H. / Mun, J.Y. / Jun, Y.W. / Park, J.H. / Lee, S.H. / Lee, S.K. / Lee, Y.K. / Song, H.K. / Lazarou, M. / Cho, D.H. / Komatsu, M. / Noda, N.N. / Jang, D.J. / Lee, J.A.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transmembrane protein 184 homolog C30D11.06c,Gamma-aminobutyric acid receptor-associated protein-like 2


Theoretical massNumber of molelcules
Total (without water)17,2531
Polymers17,2531
Non-polymers00
Water2,684149
1
A: Transmembrane protein 184 homolog C30D11.06c,Gamma-aminobutyric acid receptor-associated protein-like 2

A: Transmembrane protein 184 homolog C30D11.06c,Gamma-aminobutyric acid receptor-associated protein-like 2


Theoretical massNumber of molelcules
Total (without water)34,5062
Polymers34,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.850, 45.850, 152.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

-
Components

#1: Protein Transmembrane protein 184 homolog C30D11.06c,Gamma-aminobutyric acid receptor-associated protein-like 2 / GABA(A) receptor-associated protein-like 2 / Ganglioside expression factor 2 / GEF-2 / General ...GABA(A) receptor-associated protein-like 2 / Ganglioside expression factor 2 / GEF-2 / General protein transport factor p16 / Golgi-associated ATPase enhancer of 16 kDa / GATE-16 / MAP1 light chain 3-related protein


Mass: 17252.773 Da / Num. of mol.: 1 / Mutation: F28S V29T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast), (gene. exp.) Homo sapiens (human)
Strain: 972 / ATCC 24843 / Gene: SPAC30D11.06c, GABARAPL2, FLC3A, GEF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q09906, UniProt: P60520
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 8% PEG 3000, 0.1 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.805→43.91 Å / Num. obs: 15809 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1542 / Rpim(I) all: 0.04473 / Rrim(I) all: 0.1607 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.805-1.916.9721.2871.5246120.5971.38999
1.91-2.057.230.723.1443220.8550.776100
2.05-2.217.1230.4045.1640290.9430.436100
2.21-2.426.8840.2557.1937420.9630.276100
2.42-2.76.3030.1819.1333690.9750.197100
2.7-3.127.1110.1412.2729490.9880.152100
3.12-3.827.4710.11616.2425220.990.125100
3.82-5.387.3840.09818.719230.9950.106100
5.38-43.917.2770.08719.0210770.9950.09399.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIX1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CO7

4co7


Resolution: 1.805→43.91 Å / SU ML: 0.174 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.6936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2054 791 5 %
Rwork0.1771 15016 -
obs0.1785 15807 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.62 Å2
Refinement stepCycle: LAST / Resolution: 1.805→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 0 149 1269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611162
X-RAY DIFFRACTIONf_angle_d0.77381570
X-RAY DIFFRACTIONf_chiral_restr0.0572173
X-RAY DIFFRACTIONf_plane_restr0.0065203
X-RAY DIFFRACTIONf_dihedral_angle_d14.4306439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.805-1.920.2971280.25072429X-RAY DIFFRACTION99.49
1.92-2.070.23241280.19812431X-RAY DIFFRACTION100
2.07-2.270.22291290.17452461X-RAY DIFFRACTION100
2.27-2.60.19871310.1792481X-RAY DIFFRACTION100
2.6-3.280.21161330.18492534X-RAY DIFFRACTION100
3.28-43.910.18411420.16082680X-RAY DIFFRACTION99.89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.915253141484.600294316694.220258246825.49776897914.969279999694.54575539845-1.26627089210.3128585545070.47050446355-0.1855308055130.163681759474-0.0456949150077-0.02332398027880.4607978969991.207970669110.949633482802-0.02115754326250.03409513948280.771913819282-0.1014108076150.66900364944440.03679042353.35940592219-13.5805305779
24.9997808128-0.0826800511865-3.233783701033.18382609672-0.8491646065148.17267161378-0.228835301007-0.584989515574-0.8740548218750.260083485081-0.2777033648720.07255734076451.360606777590.2751341359350.2286172155430.5650772015830.01741333936110.1172577285620.233876629184-0.007478678505610.3640625459727.6761072271-2.36071665551-11.0099264222
32.661952853270.881593156998-4.328130564430.808864039947-1.769493409267.23508119017-0.07590414764521.0391848279-0.274051886357-1.051950596370.5940368831220.114641252829-0.255658526434-1.034864556670.03439899767270.575142975794-0.0897225962515-0.03806520441730.45589217155-0.01827165505880.32648170680516.322201545-2.45127648909-0.613541733104
44.338876895950.87893911566-1.929895636554.30041057572-0.2352824612295.663979851420.187702165675-0.1306185538990.8213973659460.159051662258-0.002060703059390.425712132431-0.471842178678-0.139767211082-0.002098694394930.2098900657970.0128900425022-0.01907637134280.198739140157-0.04441632365080.24290246048113.7835752805-4.1464967661718.3480961324
52.04108296242-0.918262037982-0.4445149532562.988961471751.318991604344.12972192377-0.01398543261040.1524568537690.111387677608-0.341207979899-0.04859453482020.1178638590190.0209752616533-0.2155675897420.1288480304880.169313249288-0.0211489195286-0.0049259166120.171997062296-0.01202991417260.2155884165759.99331684898-13.87934841795.44589947668
61.7831974133-0.326794644811-0.03047266779693.025323801121.352923443394.25666940167-0.05679574749060.0448399316456-0.1884992468950.0332262886252-0.1693855448570.4086309885060.161698412786-0.2518502002530.2421681348050.173686373919-0.01898711413430.04334698827640.227298012025-0.05177649611350.2572747946835.45544467011-20.87066972518.56981683158
72.2761301458-0.2039222961060.3740048244953.046980795971.030653373763.99843605689-0.1046504099730.0377630949411-0.116990349034-0.02757012580790.08921121163610.1250069386560.03900270887990.03330846834810.08113018153170.1655622084880.01661413683630.04347681656440.162590415686-0.01340854186710.21129935302913.4928018781-25.11795349183.55044483545
84.70492623757-0.0391409889526-1.60863890775.82781040702-0.7279175651363.60341926804-0.16263188046-0.6589830723710.09757639199310.585565276762-0.0436083448327-0.3176919265820.140852293070.4113670754050.1675676135210.286896929420.01458007690580.006992964145530.3119996394840.009654655402340.26041867934616.6139330187-20.546032017817.6107666218
92.09246140501-0.676843009618-1.477685858262.748106183220.5349293044963.98357429140.07780770672370.202998531558-0.0235998434097-0.10243562886-0.2463967017560.09921460561190.362935900193-0.3643641881090.1140526211940.1143016686610.0284370182657-0.01093341225590.1429423010860.02007155984620.14590019408916.8013591089-18.21169995610.948396483161
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 7 )1 - 71 - 7
22chain 'A' and (resid 8 through 17 )8 - 178 - 17
33chain 'A' and (resid 18 through 35 )18 - 3518 - 31
44chain 'A' and (resid 36 through 49 )36 - 4932 - 45
55chain 'A' and (resid 50 through 72 )50 - 7246 - 68
66chain 'A' and (resid 73 through 93 )73 - 9369 - 89
77chain 'A' and (resid 94 through 115 )94 - 11590 - 111
88chain 'A' and (resid 116 through 123 )116 - 123112 - 119
99chain 'A' and (resid 124 through 144 )124 - 144120 - 140

+
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