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- PDB-7bru: Crystal structure of human RTN3 LIR fused to human GABARAP -

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Basic information

Entry
Database: PDB / ID: 7bru
TitleCrystal structure of human RTN3 LIR fused to human GABARAP
ComponentsReticulon-3,Gamma-aminobutyric acid receptor-associated protein
KeywordsMEMBRANE PROTEIN / autophagy / endoplasmic reticulum
Function / homology
Function and homology information


endoplasmic reticulum tubular network formation / endoplasmic reticulum tubular network organization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / Synaptic adhesion-like molecules / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex ...endoplasmic reticulum tubular network formation / endoplasmic reticulum tubular network organization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / Synaptic adhesion-like molecules / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / negative regulation of amyloid-beta formation / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / vesicle-mediated transport / sperm midpiece / viral process / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / membrane => GO:0016020 / lysosome / Golgi membrane / apoptotic process / ubiquitin protein ligase binding / synapse / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular space / plasma membrane / cytosol
Similarity search - Function
Reticulon / Reticulon / Reticulon domain profile. / 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
PHOSPHATE ION / Gamma-aminobutyric acid receptor-associated protein / Reticulon-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsYamasaki, A. / Noda, N.N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K18339 Japan
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Science and TechnologyJPMJCR13M7 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes.
Authors: Mochida, K. / Yamasaki, A. / Matoba, K. / Kirisako, H. / Noda, N.N. / Nakatogawa, H.
History
DepositionMar 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulon-3,Gamma-aminobutyric acid receptor-associated protein
B: Reticulon-3,Gamma-aminobutyric acid receptor-associated protein
C: Reticulon-3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2469
Polymers48,6763
Non-polymers5706
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-81 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.418, 137.418, 67.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-93-

ARG

21B-201-

PO4

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Components

#1: Protein Reticulon-3,Gamma-aminobutyric acid receptor-associated protein / Homolog of ASY protein / HAP / Neuroendocrine-specific protein-like 2 / NSP-like protein 2 / ...Homolog of ASY protein / HAP / Neuroendocrine-specific protein-like 2 / NSP-like protein 2 / Neuroendocrine-specific protein-like II / NSPLII / GABA(A) receptor-associated protein / MM46


Mass: 16225.479 Da / Num. of mol.: 3 / Mutation: F3S,V4T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTN3, GABARAP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95197, UniProt: O95166
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M potassium phosphate monobasic, 0.8 M sodium phosphate monobasic, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.149→48.131 Å / Num. obs: 35698 / % possible obs: 99.87 % / Redundancy: 13.2 % / Biso Wilson estimate: 47.13 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07233 / Rpim(I) all: 0.02083 / Rrim(I) all: 0.07533 / Net I/σ(I): 20.14
Reflection shellResolution: 2.149→2.226 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.8381 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 3473 / CC1/2: 0.935 / CC star: 0.983 / Rpim(I) all: 0.2356 / Rrim(I) all: 0.8711 / % possible all: 99.28

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 2.149→48.131 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.77
RfactorNum. reflection% reflection
Rfree0.2299 1785 5 %
Rwork0.2062 --
obs0.2074 35689 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.149→48.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 30 96 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083381
X-RAY DIFFRACTIONf_angle_d0.8664583
X-RAY DIFFRACTIONf_dihedral_angle_d13.3862017
X-RAY DIFFRACTIONf_chiral_restr0.059481
X-RAY DIFFRACTIONf_plane_restr0.006596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.149-2.20670.33911320.28052522X-RAY DIFFRACTION99
2.2067-2.27170.28411350.24982551X-RAY DIFFRACTION100
2.2717-2.3450.28311360.24052580X-RAY DIFFRACTION100
2.345-2.42880.26761350.23192567X-RAY DIFFRACTION100
2.4288-2.52610.26891360.23952585X-RAY DIFFRACTION100
2.5261-2.6410.26211360.24412577X-RAY DIFFRACTION100
2.641-2.78020.2511360.2352585X-RAY DIFFRACTION100
2.7802-2.95440.23161360.23452599X-RAY DIFFRACTION100
2.9544-3.18250.25471380.23262605X-RAY DIFFRACTION100
3.1825-3.50260.22941370.20792615X-RAY DIFFRACTION100
3.5026-4.00930.22711390.19962634X-RAY DIFFRACTION100
4.0093-5.05040.19341400.16332671X-RAY DIFFRACTION100
5.0504-48.1310.21311490.19762813X-RAY DIFFRACTION100
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)
16.6128-0.3473-3.2734.62440.40275.64420.07320.23920.3342-0.13540.0258-0.576-0.14960.1262-0.03610.4315-0.0511-0.01030.3020.03950.497731.3814-57.93891.4234
23.6383-3.0084-5.99632.44754.93879.9272-0.4635-0.9923-0.8174-0.5162-0.04950.35532.27270.13190.36420.7851-0.03960.0910.53020.14940.630421.7106-56.220818.9865
39.0583-1.26582.874.0659-0.74414.47430.0476-0.2203-0.81160.1161-0.01960.33610.45420.0276-0.00720.4385-0.0385-0.00910.42030.08710.57746.3106-59.49625.059
44.42281.3036-2.53883.0429-0.72791.32160.3503-0.17870.23620.0394-0.15530.2208-0.15530.0434-0.18960.31410.0124-0.00810.35790.04250.349.0501-45.87322.0785
58.9271.82385.39032.16461.47853.34550.3140.32791.11070.3528-0.64150.1441-0.06110.95490.41460.4757-0.04380.03480.45530.03490.54279.4409-36.859918.9555
63.5049-0.6428-0.14952.52774.40598.19860.50250.39541.82610.174-0.6135-0.2952-0.753-0.12440.02530.5392-0.08410.07550.56350.06220.924617.6211-34.5819.89
74.17581.6148-0.32195.0287-0.86623.6-0.0390.27-0.4055-0.49220.162-0.16070.10090.2346-0.12570.37190.00470.01970.3527-0.03880.394413.678-49.744414.6981
85.57640.53173.62521.298-1.89736.3832-0.69570.0830.70810.17620.69240.27410.11830.4993-0.04511.89450.3102-0.76481.23660.24321.214212.6677-20.8877-12.0448
94.15615.16120.58036.44011.08924.7284-1.04471.751-0.3197-2.13031.5154-0.0675-3.0228-0.0483-0.22991.8485-0.0857-0.31651.1537-0.17031.155323.7335-31.639-14.6167
104.8267-0.256-3.85874.92352.90175.6704-0.23760.67830.0814-0.3163-0.091-0.1311-0.57860.04230.29020.7302-0.31980.00460.71070.06730.415238.822-40.6315-10.1856
115.93267.1976-3.97059.4607-4.20163.5383-0.35990.5060.0718-0.72250.39710.0209-0.06580.1859-0.03360.6513-0.19680.06270.5645-0.04870.35234.486-53.5243-16.1109
123.04841.7553-0.53324.77131.8483.0173-0.21120.12890.1902-0.30840.13880.2796-0.1528-0.00650.05070.3869-0.0646-0.01970.33570.04790.335229.869-45.2589-0.1132
132.9432-0.56591.3988.6177-5.63856.55050.2013-0.1422-0.04870.1784-0.25020.2348-0.19060.3135-0.0580.32640.02340.04380.49380.03450.4757-0.3679-42.033521.6425
141.11160.8643-0.79630.8776-1.0981.64250.60220.84961.5482-0.0407-0.3420.9057-0.61260.2567-0.43020.80850.2285-0.08430.7547-0.24751.96492.8507-24.053112.2605
152.07790.28290.19790.39070.24521.9973-0.4070.34671.5294-0.82220.21171.1973-0.35890.05690.09831.21440.2111-0.51241.0850.07011.9875-1.3705-17.4542-3.7064
165.035-1.5831.63235.31130.64825.0352-0.6490.03550.1396-0.83850.11511.2455-0.6303-0.32080.29680.96780.0699-0.31060.72620.08311.160611.332-20.9272-0.6689
174.5474-2.96551.03574.44371.30952.2818-0.5112-0.12610.1011-1.4351-0.00952.5171-0.5563-0.26230.37320.84420.0479-0.3340.56250.10081.245117.2849-27.9912-0.6287
181.6217-1.0328-0.84641.0471-0.14291.6623-0.11-0.23280.2492-0.12330.19171.33550.3846-1.0817-0.04610.957-0.039-0.55611.17520.26932.10734.3784-33.284-3.335
193.7324-0.3541-1.33890.25720.20860.9447-0.1886-0.2468-1.08460.20710.60242.9313-0.061-0.3175-0.39940.89120.2322-0.0710.75920.28991.89648.0248-25.05394.9008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 101 )
7X-RAY DIFFRACTION7chain 'A' and (resid 102 through 138 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 32 )
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 46 )
12X-RAY DIFFRACTION12chain 'B' and (resid 47 through 138 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 18 )
14X-RAY DIFFRACTION14chain 'C' and (resid 19 through 25 )
15X-RAY DIFFRACTION15chain 'C' and (resid 26 through 46 )
16X-RAY DIFFRACTION16chain 'C' and (resid 47 through 69 )
17X-RAY DIFFRACTION17chain 'C' and (resid 70 through 112 )
18X-RAY DIFFRACTION18chain 'C' and (resid 113 through 120 )
19X-RAY DIFFRACTION19chain 'C' and (resid 121 through 138 )

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