[English] 日本語
Yorodumi
- PDB-8q7k: IRGQ LIR2 peptide in complex with LC3B -

+
Open data


ID or keywords:

Loading...

-
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


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 / autophagosome membrane ...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 / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / endomembrane system / autophagosome / Pexophagy / 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 / microtubule binding / cytoplasmic vesicle / microtubule / ubiquitin protein ligase binding / GTP 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more