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- PDB-8q7k: IRGQ LIR2 peptide in complex with LC3B -

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Basic information

Entry
Database: PDB / ID: 8q7k
TitleIRGQ LIR2 peptide in complex with LC3B
Components
  • Immunity-related GTPase family Q protein
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / Autophagy / LC3B / LIR / IRGQ
Function / homology
Function and homology information


substrate localization to autophagosome / SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane ...substrate localization to autophagosome / SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / protein quality control for misfolded or incompletely synthesized proteins / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / positive regulation of autophagy / endomembrane system / Pexophagy / autophagosome / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / mitochondrial membrane / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / protein-macromolecule adaptor activity / microtubule binding / microtubule / lysosome / ubiquitin protein ligase binding / mitochondrion / cytosol
Similarity search - Function
Immunity-related GTPase family Q protein / IRG-type guanine nucleotide-binding (G) domain / IRG-type guanine nucleotide-binding (G) domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Immunity-related GTPase family Q protein / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMisra, M. / Bailey, H.J. / Pomirska, J. / Dikic, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)259130777 Germany
CitationJournal: Cell / Year: 2024
Title: IRGQ-mediated autophagy in MHC class I quality control promotes tumor immune evasion.
Authors: Herhaus, L. / Gestal-Mato, U. / Eapen, V.V. / Macinkovic, I. / Bailey, H.J. / Prieto-Garcia, C. / Misra, M. / Jacomin, A.C. / Ammanath, A.V. / Bagaric, I. / Michaelis, J. / Vollrath, J. / ...Authors: Herhaus, L. / Gestal-Mato, U. / Eapen, V.V. / Macinkovic, I. / Bailey, H.J. / Prieto-Garcia, C. / Misra, M. / Jacomin, A.C. / Ammanath, A.V. / Bagaric, I. / Michaelis, J. / Vollrath, J. / Bhaskara, R.M. / Bundgen, G. / Covarrubias-Pinto, A. / Husnjak, K. / Zoller, J. / Gikandi, A. / Ribicic, S. / Bopp, T. / van der Heden van Noort, G.J. / Langer, J.D. / Weigert, A. / Harper, J.W. / Mancias, J.D. / Dikic, I.
History
DepositionAug 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: Microtubule-associated proteins 1A/1B light chain 3B
C: Immunity-related GTPase family Q protein
D: Immunity-related GTPase family Q protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7805
Polymers31,7184
Non-polymers621
Water3,621201
1
A: Microtubule-associated proteins 1A/1B light chain 3B
C: Immunity-related GTPase family Q protein


Theoretical massNumber of molelcules
Total (without water)15,8592
Polymers15,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Immunity-related GTPase family Q protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9213
Polymers15,8592
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.423, 68.423, 118.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 9 or resid 11 through 75 or resid 77 through 117))
d_2ens_1(chain "B" and (resid 4 through 9 or resid 11 through 75 or resid 77 through 117))
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUGLNGLNAA4 - 94 - 9
d_12ens_1ARGARGALAALAAA11 - 7511 - 75
d_13ens_1GLNGLNGLUGLUAA77 - 11777 - 117
d_21ens_1GLUGLUGLNGLNBB4 - 94 - 9
d_22ens_1ARGARGALAALABB11 - 7511 - 75
d_23ens_1GLNGLNGLUGLUBB77 - 11777 - 117
d_11ens_2GLUGLUGLUGLUCC417 - 4251 - 9
d_21ens_2GLUGLUGLUGLUDD417 - 4251 - 9

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.648557137317, -0.761162699048, -0.00223275905829), (-0.76114864612, -0.648559375675, 0.00484507322005), (-0.00513596583013, -0.00144284528336, -0.999985769925)12.4108317188, 26.0198738103, 16.7669030443
2given(0.674238535619, -0.723656875598, 0.147387663957), (-0.692932428382, -0.688925695535, -0.212664138322), (0.255435014794, 0.0412566653017, -0.965945568231)9.80055687253, 26.491383345, 12.6286553506

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14710.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Protein/peptide Immunity-related GTPase family Q protein


Mass: 1149.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WZA9
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1 M lithium chloride, 0.1 M citrate, 20% PEG 6000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→48.38 Å / Num. obs: 37749 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 27.65 Å2 / CC1/2: 1 / Net I/σ(I): 19.66
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 7386 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→24.19 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 1883 4.99 %
Rwork0.1917 35828 -
obs0.1927 37711 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.74 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 4 201 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142156
X-RAY DIFFRACTIONf_angle_d1.16692906
X-RAY DIFFRACTIONf_chiral_restr0.0847324
X-RAY DIFFRACTIONf_plane_restr0.0126375
X-RAY DIFFRACTIONf_dihedral_angle_d16.9702844
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.07040569499
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS5.3409061779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.33521420.30022703X-RAY DIFFRACTION99.75
1.64-1.690.27541530.26252678X-RAY DIFFRACTION99.86
1.69-1.750.22161320.23322716X-RAY DIFFRACTION99.96
1.75-1.810.25151410.22842718X-RAY DIFFRACTION99.93
1.81-1.880.26451430.22032709X-RAY DIFFRACTION99.93
1.88-1.970.25751630.21342715X-RAY DIFFRACTION99.97
1.97-2.070.2061400.19562738X-RAY DIFFRACTION99.86
2.07-2.20.20951410.18752745X-RAY DIFFRACTION99.97
2.2-2.370.23541350.19522744X-RAY DIFFRACTION99.93
2.37-2.610.23621540.19722758X-RAY DIFFRACTION99.93
2.61-2.980.24871330.20032799X-RAY DIFFRACTION100
2.98-3.760.19031460.17882830X-RAY DIFFRACTION99.97
3.76-24.190.18351600.1762975X-RAY DIFFRACTION99.59
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)
13.112339678010.1983209086040.1800957659894.459487803781.133962401343.20106392652-0.2760009855770.179232693121-0.400768708761-0.07144255503020.309175390491-0.3074108476080.2074969082420.000922271235906-0.07626689243340.20379462265-0.03635099050960.04643291622330.179764276919-0.01405408736170.19194665597131.6713737567-17.2616233246-2.2345329831
22.5443028265-0.429958894073-0.7374458133062.543086495631.104192203615.51699739393-0.0220343381214-0.1910461877610.1195061085180.1872229161890.02941472252190.0656759348931-0.08532415191380.0668392485660.0007616054887080.227749716684-0.0494651843028-0.002840705902520.185417164201-0.01352807305250.25678040755724.1528652141-8.9956286913210.8891793948
38.067107067351.00027544047-0.6497065259597.39734877674-3.424591329882.170753885280.0508002408490.8787773520520.494210920693-0.657346422946-0.453094497231-0.2303155399530.4515249050620.7167004990060.3616193302920.258182671301-0.008294570554840.01147895342570.3580175403550.09071259318450.28818023436550.984679305310.397925051210.8271143931
43.80899532769-5.02759158852-1.019908726416.802518120920.6757793346843.09268628679-0.205888948618-0.7852246167470.4571534825510.5664558190650.229565770613-0.456875543944-0.2140559044870.15630214366-0.0705945488920.368949001975-0.0932950216123-0.025003824610.348131888304-0.01885197709410.25705856357742.97038240114.749446958923.4568420977
55.8052237299-1.10426894945-3.58105908943.638002021672.258431875942.934553200660.0330462951301-0.123276791480.233191804280.4553147911680.1585561894880.127243868731-0.0372778386262-0.318668249896-0.3426380421160.30873162713-0.003767701564150.04887411651160.2661148356430.01619726757370.23857047469937.143240402516.548806385613.312034986
65.229892260851.320525172891.050277842642.526310148162.376245993482.37118333860.1855944942290.499649456044-0.4582308053130.2362073880490.207930271519-0.3062504674080.5254176760020.73312480535-0.3530026897550.3549679612540.01436004896360.01308583943770.253245518519-0.05688123296740.30395256787844.021724514.0300646968-0.857197289055
77.408181253160.9345075371611.063524215975.148887384030.7603316500045.698450957040.150779081891-0.557804859550.6798377398950.229038478749-0.1751828893950.403478488439-0.575575960072-0.5935521554350.06654131611360.3217704637090.0490085431960.08009126530640.326858359956-0.004254406071030.30003972941231.620573015719.626010760812.4706667867
89.390889328881.61231187121-4.974430982355.95171612986-1.98291391652.943286321670.1688590319770.04383106464090.4543685829240.120268683516-0.1103096093090.633767273582-0.381934577975-0.426817651971-0.01283463330180.215748937741-8.83517006083E-5-0.02981333284350.252574257125-0.01473691158260.39785571798631.607649112719.43310068611.75401330977
94.582336806310.75198479370.8505845955572.943257652661.838985221932.01144365718-0.2466789619420.436050392510.604941677109-0.8186548765020.02518276084780.256175326-0.221107128926-0.2838716341260.2132750396370.325369895492-0.0508875479609-0.05780177156680.2562849169040.05974282785370.29527300214233.3633503614.9308253813-5.1434764717
101.44299003421.371552540981.436051147331.740209580210.397243730964.32888880077-0.296067707192-0.42327487843-0.721884718557-0.3692408728290.1955509850260.5227193596171.54172901064-0.9611807442690.2360988766140.658697450406-0.1954802867690.05082380232730.5540027100310.008073323030860.67655001694128.04493568157.048866805536.47402762746
112.191677679140.763999577562-0.7171244596051.42251102912-0.2152282150415.135470331970.103385682303-0.1978191457820.00508982312830.1255647807860.001916143260880.210044249860.0072980671358-0.314241584968-0.1057300769750.254811289061-0.0323447286680.01491835917580.1939508644230.02522386158340.23929770861535.18118529689.1470860983713.4486144269
127.70947265683-6.46376007569-2.325353820865.841530949173.08271799613.72470199027-0.3476048903860.289247264822-0.663287713267-0.5445741382340.04063522684310.1732187077980.2151997062240.2736383806130.1717058523970.6033718894290.1182522281670.07146785418140.605994028885-0.03658758544280.4241891572338.55860330713.91607874833-7.65781912714
133.15474485793-3.24048089848-0.6620108058783.480187763651.084958683622.521846527860.0144486122316-0.551794541473-0.1907574263490.4493380178970.263797038148-0.007342761540060.2983230185330.374786849688-0.1406642650110.279870421936-0.0489694980410.01033787613590.2882930529790.006044474298390.29943034459421.9727522741-20.91685090733.57939488074
142.493637183-3.557627247770.9554971933945.38772886387-1.331507688752.97865170717-0.634975616576-0.2527671179921.68378642460.2052799090810.310756335596-0.295861493147-1.339832887610.5630736732750.3716070816530.572642577896-0.1139901675120.001351139164340.3418568705320.03669721657930.60143989570340.204519390624.962432626313.9264498517
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 26 )AA4 - 261 - 23
22chain 'A' and (resid 27 through 118 )AA27 - 11824 - 115
33chain 'B' and (resid 3 through 12 )BB3 - 121 - 10
44chain 'B' and (resid 13 through 26 )BB13 - 2611 - 24
55chain 'B' and (resid 27 through 37 )BB27 - 3725 - 35
66chain 'B' and (resid 38 through 50 )BB38 - 5036 - 48
77chain 'B' and (resid 51 through 59 )BB51 - 5949 - 57
88chain 'B' and (resid 60 through 71 )BB60 - 7158 - 69
99chain 'B' and (resid 72 through 83 )BB72 - 8370 - 81
1010chain 'B' and (resid 84 through 94 )BB84 - 9482 - 92
1111chain 'B' and (resid 95 through 114 )BB95 - 11493 - 112
1212chain 'B' and (resid 115 through 119 )BB115 - 119113 - 117
1313chain 'C' and (resid 417 through 425 )CD417 - 4251 - 9
1414chain 'D' and (resid 417 through 425 )DE417 - 4251 - 9

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