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- PDB-7ved: Crystal structure of GABARAP fused to TEX264 LIR with S272D mutation -

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Basic information

Entry
Database: PDB / ID: 7ved
TitleCrystal structure of GABARAP fused to TEX264 LIR with S272D mutation
ComponentsTestis-expressed protein 264,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / Autophagy / ER-phagy
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / protein-DNA covalent cross-linking repair / phosphatidylethanolamine binding / reticulophagy / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / autophagy of mitochondrion ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / protein-DNA covalent cross-linking repair / phosphatidylethanolamine binding / reticulophagy / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / smooth endoplasmic reticulum / protein targeting / sperm midpiece / autophagosome / platelet alpha granule lumen / replication fork / microtubule cytoskeleton organization / protein transport / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / signaling receptor activity / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Regulatory factor, effector binding domain superfamily / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Testis-expressed protein 264
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsYamasaki, A. / Noda, N.N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20E3 Japan
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Society for the Promotion of Science (JSPS)20K06637 Japan
CitationJournal: Embo Rep. / Year: 2022
Title: Phosphorylation by casein kinase 2 enhances the interaction between ER-phagy receptor TEX264 and ATG8 proteins.
Authors: Chino, H. / Yamasaki, A. / Ode, K.L. / Ueda, H.R. / Noda, N.N. / Mizushima, N.
History
DepositionSep 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Testis-expressed protein 264,Gamma-aminobutyric acid receptor-associated protein
B: Testis-expressed protein 264,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6395
Polymers30,3502
Non-polymers2883
Water2,702150
1
A: Testis-expressed protein 264,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3673
Polymers15,1751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-21 kcal/mol
Surface area8120 Å2
MethodPISA
2
B: Testis-expressed protein 264,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2712
Polymers15,1751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.364, 82.628, 102.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARG(chain 'A' and (resid -12 through -11 or (resid -10...AA-12 - 141 - 27
12SERSERASPASP(chain 'A' and (resid -12 through -11 or (resid -10...AA16 - 2729 - 40
13VALVALVALVAL(chain 'A' and (resid -12 through -11 or (resid -10...AA29 - 8042 - 93
14ASNASNTYRTYR(chain 'A' and (resid -12 through -11 or (resid -10...AA82 - 11595 - 128
25GLYGLYARGARG(chain 'B' and (resid -12 through 14 or resid 16...BB-12 - 141 - 27
26SERSERASPASP(chain 'B' and (resid -12 through 14 or resid 16...BB16 - 2729 - 40
27VALVALVALVAL(chain 'B' and (resid -12 through 14 or resid 16...BB29 - 8042 - 93
28ASNASNTYRTYR(chain 'B' and (resid -12 through 14 or resid 16...BB82 - 11595 - 128

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Components

#1: Protein Testis-expressed protein 264,Gamma-aminobutyric acid receptor-associated protein / Putative secreted protein Zsig11 / GABA(A) receptor-associated protein / MM46


Mass: 15175.160 Da / Num. of mol.: 2 / Mutation: S272D,F3S,V4T
Source method: isolated from a genetically manipulated source
Details: GABARAP with F3S and V4T mutations fused to TEX264 LIR with S272D mutation
Source: (gene. exp.) Homo sapiens (human) / Gene: TEX264, ZSIG11, UNQ337/PRO536, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6I9, UniProt: O95166
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium sodium tartrate, 0.1M sodium citrate pH 5.6, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 95 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: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.02→41.31 Å / Num. obs: 21898 / % possible obs: 99.29 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.07
Reflection shellResolution: 2.02→2.093 Å / Mean I/σ(I) obs: 1.68 / Num. unique obs: 1990 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 2.02→41.31 Å / SU ML: 0.2202 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.0225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 1095 5 %
Rwork0.1876 20803 -
obs0.1895 21898 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.75 Å2
Refinement stepCycle: LAST / Resolution: 2.02→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 15 150 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752205
X-RAY DIFFRACTIONf_angle_d0.93872986
X-RAY DIFFRACTIONf_chiral_restr0.0664305
X-RAY DIFFRACTIONf_plane_restr0.0061395
X-RAY DIFFRACTIONf_dihedral_angle_d13.8385828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.110.32441270.27142426X-RAY DIFFRACTION95.19
2.11-2.220.28431350.22772560X-RAY DIFFRACTION100
2.22-2.360.2581360.21312580X-RAY DIFFRACTION99.89
2.36-2.550.24661360.20632587X-RAY DIFFRACTION99.85
2.55-2.80.24051370.18912598X-RAY DIFFRACTION99.93
2.8-3.210.22951380.18252635X-RAY DIFFRACTION99.96
3.21-4.040.19231390.1572638X-RAY DIFFRACTION99.89
4.04-41.310.21121470.18672779X-RAY DIFFRACTION99.66
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)
11.50026499365-0.142902517049-0.6213505075057.28019001918-5.066913870953.80516709051-0.2103577355680.333760360229-0.0729414060896-1.01682194137-0.0678337850256-0.2663622755120.805766204688-0.1656140566780.2887928449440.445609391486-0.000806316229460.01933488054370.356256546327-0.05683748700130.25807958359622.16944021177.75771918061-21.1788259164
24.014844678966.32613204699-1.045309340562.01435638007-2.667476943666.443195987680.07055830492480.106408835596-0.2955792147140.488649429414-0.287698235725-0.4519704736710.1729791936470.3154841498770.1898912555920.331304089315-0.00151518960002-0.0407316549940.280629102119-0.01397276124210.32761283754317.1748772134-9.24496910738-7.36229207214
39.72391467486-8.1896316427-7.541508197878.964135376377.119917132476.00185306834-0.03806750094880.219027825969-0.3971741976760.235102053744-0.3517951953180.6544754171460.170022200187-0.2664264511380.5324109884170.280689942059-0.0928321995748-0.03500763974480.359859316743-0.04767324624740.3686996000364.65731704885-6.22006781676-5.05719665722
45.838376300021.3932528381-1.630392726193.421847357730.8865061909574.08582931267-0.212992147589-0.308837765276-0.330014250980.08567073813490.0600111853914-0.116650143180.2462582563160.1144484686150.2476384378660.2800185085060.0211603471327-0.03526475848610.2346084027680.001813519928230.23718507994216.67087649051.979098703981.51467004309
59.79593989269-5.869358533914.735391294067.228775717870.07158503165136.610422044860.1375221144970.0445812325242-0.511828134962-0.0281322974807-0.008660276675610.0259201949560.05939141647940.390069956264-0.1018545814380.2118854835420.002876850325720.0191757803630.247607979210.01574945199170.23647541611920.79308864619.112129838956.67110714572
68.45333965042-0.45850774896-0.3248125783673.718634996532.364810084024.773815555940.189510669384-0.0337491769095-0.185103272276-0.08751926350530.129934638475-0.354585544539-0.08993592167630.254382671899-0.325349433250.26210199412-0.0283134955452-0.01395174615950.1534025454930.0007906412637610.22248818969423.830495304410.6098463438-0.454161316656
78.158008863284.156498225153.93114331193.845815851423.822336824843.80431428588-0.08465386330820.2393664401350.888205429184-0.578531484609-0.4865665104440.583968258219-0.65988630234-0.4714756319330.7295492063690.374141539522-0.000375575149315-0.07825177010310.3774169919830.002422664909560.3516519359848.541944190379.67911533351-5.08351612917
84.018647453524.683741347871.876732043035.401607998111.774879801993.95156417474-0.1169348739310.644934900447-0.292848385273-0.299659908420.09754544980170.1989270311210.0857664705053-0.152590164383-0.0207622184940.3308765371280.020099307631-0.01805503571930.30632123673-0.06314937782440.28253439391413.53858406051.27930281952-6.6234017315
98.014103847282.49281276572.12602656426.820294450853.250366216122.136183142990.04492737865860.396379732870.115515393494-0.3582750943350.00332271285062-0.2700389702290.01862305562961.531890449670.01456536238990.383139071959-0.0810083664020.03050779786320.475949641045-0.04918569940160.45322202100929.60746847247.72566503315-8.05344400768
101.91184621382-3.110167031363.833762130455.6043323516-7.024845205648.81122111864-0.1153781135470.1486126419420.00958370327711.195437308610.4797191903270.29021571276-2.26103040513-0.746698561112-0.2750783459940.6952276929610.0643347368073-0.01033674409920.483023790169-0.09409919075950.4161542204858.19083367301-0.489419690436-36.6967913217
117.12120755573-4.17946369579-0.969261243447.366745245873.524009698197.46290713487-0.019075441758-0.2816723145040.2993893242420.6855520334680.171527653047-0.3586653582120.2582258646090.211009014621-0.1150762289460.321249879095-0.0307582180886-0.04562676772430.245012104267-0.01859490015910.21835035739318.8864939975-17.4400529782-17.0882363275
127.43071161745-4.272245088041.71858469366.461899968-0.9075596261566.5619492511-0.071116941123-0.186459526596-0.1063907741370.2352481057150.1653729983910.06159123553170.0956128920726-0.246414095343-0.07326131686850.205048505656-0.03599676486780.02802436591960.2080879435320.00759514186570.15972745568212.3082972623-21.4205854009-28.8058495949
136.333375313650.8918712511311.786208415197.438986102830.7509873524665.10738200425-0.0495710206554-0.1732067485750.0158345003078-0.2363690798250.02649926115920.5034955057310.159117628468-0.3633470159710.02528677348310.2407090973210.01070279224712.23295689456E-50.234956457990.0144418888380.1648409987817.6424490345-18.6856647758-37.360396183
148.95281536774-1.82771472303-0.2272119672869.806443784526.879649305314.929354624340.2834231418320.4198809217940.80695229236-0.6994020814330.118912715607-1.20069162581-0.7472470612410.405409618674-0.3144989282130.309514891776-0.04426372515080.04937097742860.3269996219710.04481650242060.40038313554422.1941606385-14.8517185236-33.511886683
153.30400360941-2.307244910233.836484003943.12765894563-2.072676912868.22888094778-0.0777156593626-0.396017108953-0.02956451056530.007039653649110.106678378496-0.00414010475115-0.417571850852-0.312901357670.05324566165620.235726288145-0.01221722533480.03431511723830.222002116224-0.06237018847980.21432815319810.9264748671-12.6080687312-28.970396923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -12 through 3 )
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 10 )
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 24 )
4X-RAY DIFFRACTION4chain 'A' and (resid 25 through 56 )
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 90 )
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 98 )
8X-RAY DIFFRACTION8chain 'A' and (resid 99 through 110 )
9X-RAY DIFFRACTION9chain 'A' and (resid 111 through 116 )
10X-RAY DIFFRACTION10chain 'B' and (resid -12 through 3 )
11X-RAY DIFFRACTION11chain 'B' and (resid 4 through 24 )
12X-RAY DIFFRACTION12chain 'B' and (resid 25 through 56 )
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 98 )
15X-RAY DIFFRACTION15chain 'B' and (resid 99 through 116 )

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