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- PDB-7yo9: Crystal structure of fusion protein of human TP53INP2 LIR and hum... -

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Basic information

Entry
Database: PDB / ID: 7yo9
TitleCrystal structure of fusion protein of human TP53INP2 LIR and human GABARAP
ComponentsTumor protein p53-inducible nuclear protein 2,Gamma-aminobutyric acid receptor-associated proteinNeoplasm
KeywordsPROTEIN TRANSPORT / Autophagy
Function / homology
Function and homology information


negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy ...negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / sperm midpiece / ubiquitin binding / macroautophagy / protein localization / PML body / microtubule cytoskeleton organization / osteoblast differentiation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein transport / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / synapse / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / nucleus / plasma membrane / cytosol
Similarity search - Function
Tumour protein p53-inducible nuclear protein / DOR family / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / PHOSPHATE ION / Gamma-aminobutyric acid receptor-associated protein / Tumor protein p53-inducible nuclear protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor protein p53-inducible nuclear protein 2,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6083
Polymers15,4531
Non-polymers1552
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.390, 46.390, 75.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Tumor protein p53-inducible nuclear protein 2,Gamma-aminobutyric acid receptor-associated protein / Neoplasm / Diabetes and obesity-regulated gene / p53-inducible protein U / PIG-U / GABA(A) receptor-associated ...Diabetes and obesity-regulated gene / p53-inducible protein U / PIG-U / GABA(A) receptor-associated protein / MM46


Mass: 15452.565 Da / Num. of mol.: 1
Fragment: Tumor protein p53-inducible nuclear protein 2(1-15), Gamma-aminobutyric acid receptor-associated protein(16-131)
Mutation: F18S,V19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53INP2, C20orf110, DOR, PINH, GABARAP, FLC3B, HT004 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IXH6, UniProt: O95166
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 10% 2-propanol, 0.1 M sodium phosphate/citric acid pH 4.2, 0.2 M lithium sulfate

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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: 1.75→46.392 Å / Num. obs: 31600 / % possible obs: 99.5 % / Redundancy: 3.554 % / Biso Wilson estimate: 43.736 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.106 / Χ2: 0.994 / Net I/σ(I): 7.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.863.5520.8041.1450510.7420.94897.9
1.86-1.983.6120.3962.4747890.8890.46799.9
1.98-2.143.5870.1944.8544820.9620.229100
2.14-2.353.5010.1247.4541370.9770.14799.8
2.35-2.623.1980.0969.537180.9830.11599.4
2.62-3.033.4790.08612.4932580.9830.10299.9
3.03-3.73.830.08615.0427940.9830.1100
3.7-5.223.790.08316.0621720.9830.09799.9
5.22-46.3923.6430.08715.8311990.9850.10299.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.75→46.39 Å / SU ML: 0.2862 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 1565 4.97 %
Rwork0.1938 29954 -
obs0.195 31519 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 9 77 1160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651120
X-RAY DIFFRACTIONf_angle_d0.79351516
X-RAY DIFFRACTIONf_chiral_restr0.0537157
X-RAY DIFFRACTIONf_plane_restr0.0059197
X-RAY DIFFRACTIONf_dihedral_angle_d17.3046419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.35191380.38312636X-RAY DIFFRACTION95.82
1.81-1.870.3361440.31232750X-RAY DIFFRACTION99.72
1.87-1.950.32671410.30172702X-RAY DIFFRACTION99.89
1.95-2.040.34541440.26772773X-RAY DIFFRACTION99.86
2.04-2.140.28291420.23122699X-RAY DIFFRACTION99.96
2.14-2.280.24121450.22752725X-RAY DIFFRACTION99.86
2.28-2.450.25191410.21752749X-RAY DIFFRACTION99.62
2.45-2.70.27221420.22232740X-RAY DIFFRACTION99.65
2.7-3.090.22121420.2112711X-RAY DIFFRACTION99.96
3.09-3.890.19721440.17742746X-RAY DIFFRACTION100
3.89-46.390.15661420.14622723X-RAY DIFFRACTION99.79
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)
16.539392007081.11498571667-1.733947255532.024312604320.04982005070724.63243721570.296617104998-0.2354258496120.213054111020.562304028230.0441679778316-0.9062393826520.7286496386580.917914036568-0.3502064727210.7574367169040.0587583389738-0.1102514561860.612204944971-0.1592903123830.64070437091617.1697131662-10.50563811430.460760809386
22.494749309812.54308990872.695261334934.461153918265.70788190767.45725531135-0.319412752833-0.100230450099-0.007799407372460.1069497782760.370223984888-0.4972417340.1310584715440.119524825605-0.1721016938770.4790024313290.1229568347850.01757105667030.366978125838-0.04889982766820.5439275652417.7976943606-4.334891901352.16284403042
39.65157138698-5.95351617758-5.376196371174.456041268484.714019320959.22397196755-0.66996656118-0.243530056249-0.8065432272421.92398385842-0.1251592433310.8529014874810.861601654928-0.1460717041870.5754987157580.602395180277-0.01097989363630.1149084514290.3125398779810.08002036765440.56875859324910.1065481201-2.8954399166412.5689346157
48.618329361892.135037976180.6602352868188.21622960871-0.30246862395.096640747420.0640616347513-0.05501367675910.175623212873-0.0129518557137-0.2478562158280.371685297645-0.128785039820.04329999355750.1652558596050.2652311178770.0776940495246-0.003886866512780.254916862883-0.01479505084530.15855073466713.56833989514.25127678787.82655725882
51.72694596862-1.491088659840.6310489739746.04460230473-3.371328480962.07855649296-0.002743297813140.111742408812-0.069433552776-0.552578332923-0.0232010724693-0.32129738976-0.1542462095470.56261871971-0.08374595003460.4524251953640.0288618201039-0.008770776953510.3694504123590.01873579939960.2323080858419.672129221722.77050037170.600520965037
66.327938567343.04793264922-3.442486181777.98719058187-4.578348577076.48233886104-0.5335494792950.730829387169-0.164371111514-0.9254130240890.4100987211880.7190146023170.334014863202-0.6600704694580.0691159520150.440463092610.0259710409176-0.1802915922610.472645809928-0.1095465186350.4478526402466.520957872210.3375756179-1.6177673054
71.116680818422.27387199455-0.04232585585679.78352958938-2.771729213752.71851609453-0.06221172601710.238275783104-0.312044014735-0.757882739604-0.255898081742-0.157219473780.2681082115320.2261898770650.3212318623270.363481554590.0486482908593-0.004899599201180.280589403359-0.03144443534310.3160765936615.35439437156.798681023270.344507447108
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 25 )8 - 258 - 25
33chain 'A' and (resid 26 through 39 )26 - 3926 - 39
44chain 'A' and (resid 40 through 82 )40 - 8240 - 82
55chain 'A' and (resid 83 through 94 )83 - 9483 - 94
66chain 'A' and (resid 95 through 113 )95 - 11395 - 113
77chain 'A' and (resid 114 through 131 )114 - 131114 - 131

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