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- PDB-7brt: Crystal structure of Sec62 LIR fused to GABARAP -

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Basic information

Entry
Database: PDB / ID: 7brt
TitleCrystal structure of Sec62 LIR fused to GABARAP
ComponentsTranslocation protein SEC62,Gamma-aminobutyric acid receptor-associated protein
KeywordsMEMBRANE PROTEIN / autophagy / endoplasmic reticulum
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / cotranslational protein targeting to membrane / regulation of Rac protein signal transduction / post-translational protein targeting to endoplasmic reticulum membrane / GABA receptor binding / phosphatidylethanolamine binding / post-translational protein targeting to membrane, translocation / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex ...positive regulation of protein K48-linked ubiquitination / cotranslational protein targeting to membrane / regulation of Rac protein signal transduction / post-translational protein targeting to endoplasmic reticulum membrane / GABA receptor binding / phosphatidylethanolamine binding / post-translational protein targeting to membrane, translocation / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Macroautophagy / beta-tubulin binding / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / smooth endoplasmic reticulum / protein targeting / mitophagy / rough endoplasmic reticulum / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / signaling receptor activity / microtubule binding / cytoplasmic vesicle / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / plasma membrane / cytosol
Similarity search - Function
Translocation protein Sec62 / Translocation protein Sec62 / 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 / Translocation protein SEC62
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translocation protein SEC62,Gamma-aminobutyric acid receptor-associated protein
B: Translocation protein SEC62,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)31,7842
Polymers31,7842
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-5 kcal/mol
Surface area15810 Å2
Unit cell
Length a, b, c (Å)42.887, 42.889, 144.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1:2 or resid 4:41 or resid...
21(chain B and (resid 1:2 or resid 4:41 or resid...

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
11GLYGLYPROPRO(chain A and (resid 1:2 or resid 4:41 or resid...AA1 - 21 - 2
12ASPASPLYSLYS(chain A and (resid 1:2 or resid 4:41 or resid...AA4 - 414 - 41
13TYRTYRLEULEU(chain A and (resid 1:2 or resid 4:41 or resid...AA43 - 6243 - 62
14LYSLYSALAALA(chain A and (resid 1:2 or resid 4:41 or resid...AA65 - 9065 - 90
15ASPASPGLYGLY(chain A and (resid 1:2 or resid 4:41 or resid...AA92 - 11092 - 110
16LEULEUGLNGLN(chain A and (resid 1:2 or resid 4:41 or resid...AA112 - 114112 - 114
17HISHISGLYGLY(chain A and (resid 1:2 or resid 4:41 or resid...AA116 - 134116 - 134
21GLYGLYPROPRO(chain B and (resid 1:2 or resid 4:41 or resid...BB1 - 21 - 2
22ASPASPLYSLYS(chain B and (resid 1:2 or resid 4:41 or resid...BB4 - 414 - 41
23TYRTYRLEULEU(chain B and (resid 1:2 or resid 4:41 or resid...BB43 - 6243 - 62
24LYSLYSALAALA(chain B and (resid 1:2 or resid 4:41 or resid...BB65 - 9065 - 90
25ASPASPGLYGLY(chain B and (resid 1:2 or resid 4:41 or resid...BB92 - 11092 - 110
26LEULEUGLNGLN(chain B and (resid 1:2 or resid 4:41 or resid...BB112 - 114112 - 114
27HISHISGLYGLY(chain B and (resid 1:2 or resid 4:41 or resid...BB116 - 134116 - 134

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Components

#1: Protein Translocation protein SEC62,Gamma-aminobutyric acid receptor-associated protein / Translocation protein 1 / hTP-1 / GABA(A) receptor-associated protein / MM46


Mass: 15891.984 Da / Num. of mol.: 2 / Mutation: T367D,F3S,V4T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC62, GABARAP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99442, UniProt: O95166
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5 M ammonium sulfate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.49
ReflectionResolution: 1.999→41.105 Å / Num. obs: 18735 / % possible obs: 99.73 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1638 / Rpim(I) all: 0.06913 / Rrim(I) all: 0.1781 / Net I/σ(I): 9.27
Reflection shellResolution: 1.999→2.071 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 1782 / CC1/2: 0.759 / CC star: 0.929 / Rpim(I) all: 0.06913 / Rrim(I) all: 0.1781 / % possible all: 98.34

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Processing

Software
NameVersionClassification
PHENIXdev_2450refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXdev_2450phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.999→41.105 Å / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 16.54
RfactorNum. reflection% reflection
Rfree0.1836 936 5 %
Rwork0.1656 --
obs0.1663 18735 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.52 Å2 / Biso mean: 31.0739 Å2 / Biso min: 7.11 Å2
Refinement stepCycle: final / Resolution: 1.999→41.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 0 291 2463
Biso mean---34.55 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072228
X-RAY DIFFRACTIONf_angle_d0.9063013
X-RAY DIFFRACTIONf_chiral_restr0.061316
X-RAY DIFFRACTIONf_plane_restr0.007397
X-RAY DIFFRACTIONf_dihedral_angle_d15.6941345
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1203X-RAY DIFFRACTION8.245TORSIONAL
12B1203X-RAY DIFFRACTION8.245TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.05910.25551410.24422699284094
2.0591-2.12550.25461450.22592739288495
2.1255-2.20140.24641440.21472725286995
2.2014-2.28940.22491430.21632719286295
2.2894-2.39350.21941470.21142766291395
2.3935-2.51950.2511420.19412787292995
2.5195-2.67710.18171430.17832724286795
2.6771-2.88330.18241460.17912725287195
2.8833-3.17260.16841400.15352701284195
3.1726-3.62970.14491390.12792753289295
3.6297-4.56550.14331500.10862704285494
4.5655-21.21080.18441460.1652756290295
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)
12.94740.5616-0.50443.9323-0.44485.9154-0.00290.00970.0261-0.11050.1186-0.5996-0.88430.95740.00680.5479-0.17660.02650.6465-0.0230.058414.150951.091938.5193
21.642-0.1311-1.65020.79931.86765.6704-0.2543-0.0005-0.32340.42020.313-0.07360.85120.349-0.01850.420.0576-0.02050.31230.02020.12265.300640.151420.7838
32.24242.8176-1.76423.6917-1.89312.3584-0.1827-0.5951-0.44670.4964-0.2193-0.55590.4220.5759-0.15010.3930.1844-0.09130.64860.06390.148321.147241.13117.434
42.2087-0.2685-0.33290.8387-0.07621.7848-0.188-0.2609-0.2161-0.10480.1272-0.13160.2562-0.04340.08310.327-0.01780.0060.32810.0250.104611.387943.39775.3943
50.6475-0.386-0.85773.3092-0.47711.50240.10090.5604-0.1066-0.0060.1929-0.18530.266-0.0538-0.26460.25750.01830.00120.3768-0.02090.10767.688747.8374-2.1829
61.9356-0.7958-0.04751.7949-0.45643.2055-0.004-0.1195-0.03520.09270.0117-0.00710.0975-0.1534-0.0250.2784-0.02690.02380.3329-0.04060.08024.728747.70578.3517
75.5399-0.8796-0.35278.18-6.61786.8039-0.3282-0.4860.46530.66240.3851-0.5633-0.11760.1187-0.04820.4147-0.0193-0.03410.3312-0.04510.2197-2.399867.3561-2.3042
84.48372.0572-3.19098.0439-4.96994.0944-0.3107-0.30760.08780.6699-0.0154-0.0802-0.4569-0.35280.09070.3001-0.03510.01020.4287-0.01540.1132-6.712855.08238.5688
92.3105-0.7249-0.16176.5927-0.50971.4566-0.66040.1359-0.186-0.30680.30960.95680.3396-0.2181-0.05090.35840.041-0.10540.6154-0.10110.1388-18.460561.640120.2027
102.97534.30374.44346.32426.2996.7087-0.62970.12840.3624-0.85190.31890.4846-1.1280.34090.30830.51510.0175-0.14630.4548-0.00140.2483-12.669874.95219.0151
112.59271.482-1.04323.7764-2.92813.9259-0.1450.57770.2180.37330.31540.0711-0.64420.0307-0.11280.3483-0.0071-0.02590.3208-0.01190.1147-8.666669.395728.1428
120.5733-0.28810.58592.0414-0.14210.7724-0.00390.0208-0.05850.12150.020.0871-0.2084-0.0631-0.0050.34580.0333-0.00320.36-0.00630.0878-6.427260.026432.3637
130.55950.08450.14581.29690.52820.23720.09380.26920.0693-0.5060.0580.3095-0.02540.09010.02890.34420.0651-0.03140.3755-0.0390.1018-9.607964.156321.79
140.971-0.9462-2.12621.37063.28557.9319-0.73230.12730.0845-0.49240.40840.12660.3568-0.4710.18670.3224-0.07940.00160.32560.00620.1438-9.883247.92528.2208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )A1 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 28 )A10 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 42 )A29 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 74 )A43 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 86 )A75 - 86
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 134 )A87 - 134
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 9 )B1 - 9
8X-RAY DIFFRACTION8chain 'B' and (resid 10 through 17 )B10 - 17
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 28 )B18 - 28
10X-RAY DIFFRACTION10chain 'B' and (resid 29 through 42 )B29 - 42
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 53 )B43 - 53
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 116 )B54 - 116
13X-RAY DIFFRACTION13chain 'B' and (resid 117 through 128 )B117 - 128
14X-RAY DIFFRACTION14chain 'B' and (resid 129 through 134 )B129 - 134

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