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- PDB-6tbe: LC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-h... -

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Basic information

Entry
Database: PDB / ID: 6tbe
TitleLC3A in complex with (3R,4S,5R,6R)-5-hydroxy-6-((4-hydroxy-3-(4-hydroxy-3-isopentylbenzamido)-8-methyl-2-oxo-2H-chromen-7-yl)oxy)-3-methoxy-2,2-dimethyltetrahydro-2H-pyran-4-yl carbamate
ComponentsMicrotubule-associated proteins 1A/1B light chain 3A
KeywordsHYDROLASE / Inhibitor / Complex / LC3A / autophagy
Function / homology
Function and homology information


cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / phosphatidylethanolamine binding / response to iron(II) ion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade ...cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / phosphatidylethanolamine binding / response to iron(II) ion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade / organelle membrane / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / JNK cascade / cellular response to copper ion / PINK1-PRKN Mediated Mitophagy / cellular response to amino acid starvation / cellular response to starvation / macroautophagy / response to lead ion / phospholipid binding / cellular response to hydrogen peroxide / late endosome / microtubule binding / microtubule / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
NOVOBIOCIN / Microtubule-associated proteins 1A/1B light chain 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67008040045 Å
AuthorsKramer, J.S. / Pogoryelov, D. / Hartmann, M. / Chaikuad, A. / Proschak, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchDeutsches Konsortium fuer Translationale Krebsforschung Germany
German Research FoundationPR 1405/4-1 Germany
CitationJournal: J.Med.Chem. / Year: 2021
Title: Demonstrating Ligandability of the LC3A and LC3B Adapter Interface.
Authors: Hartmann, M. / Huber, J. / Kramer, J.S. / Heering, J. / Pietsch, L. / Stark, H. / Odadzic, D. / Bischoff, I. / Furst, R. / Schroder, M. / Akutsu, M. / Chaikuad, A. / Dotsch, V. / Knapp, S. / ...Authors: Hartmann, M. / Huber, J. / Kramer, J.S. / Heering, J. / Pietsch, L. / Stark, H. / Odadzic, D. / Bischoff, I. / Furst, R. / Schroder, M. / Akutsu, M. / Chaikuad, A. / Dotsch, V. / Knapp, S. / Biondi, R.M. / Rogov, V.V. / Proschak, E.
History
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7704
Polymers14,0331
Non-polymers7373
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint8 kcal/mol
Surface area7440 Å2
Unit cell
Length a, b, c (Å)95.738, 95.738, 34.647
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 14033.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H492
#2: Chemical ChemComp-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside


Mass: 612.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C31H36N2O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammoniumnitrat and 20% w/v PEG 3350 / PH range: 6-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.67→47.869 Å / Num. obs: 18199 / % possible obs: 98.39 % / Redundancy: 13.8 % / Biso Wilson estimate: 26.9789688009 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.04498 / Rpim(I) all: 0.01285 / Rrim(I) all: 0.04686 / Net I/σ(I): 32.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.67-1.797.3050.6152.862950.8740.66197.5
1.79-1.937.0780.3165.7558720.9550.34197.4
1.93-2.116.9440.15311.3154240.9890.16598.2
2.11-2.367.3310.08720.4549430.9970.09498.7
2.36-2.737.0790.05729.9243620.9980.06199.2
2.73-3.347.0270.03546.436720.9990.03798.4
3.34-4.717.190.02468.38289210.02699.7
4.71-47.8696.9970.02271.89156410.02497.9

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAL

3wal


Resolution: 1.67008040045→47.869 Å / SU ML: 0.179648712907 / Cross valid method: FREE R-VALUE / σ(F): 1.3740483431 / Phase error: 22.1261074032
RfactorNum. reflection% reflectionSelection details
Rfree0.212197763923 1749 4.98475218742 %Random selection
Rwork0.186062076115 ---
obs0.187369648755 18199 98.2911729277 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.9637307029 Å2
Refinement stepCycle: LAST / Resolution: 1.67008040045→47.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 52 97 1108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01094210310141070
X-RAY DIFFRACTIONf_angle_d0.9882720623341453
X-RAY DIFFRACTIONf_chiral_restr0.0552765735278155
X-RAY DIFFRACTIONf_plane_restr0.00512313268387187
X-RAY DIFFRACTIONf_dihedral_angle_d26.0043791132419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6701-1.71920.273134976621390.2773530981052691X-RAY DIFFRACTION95.9322033898
1.7192-1.77470.2589373427471470.2967410395932803X-RAY DIFFRACTION98.7282463186
1.7747-1.83820.2595505373571430.252268133712764X-RAY DIFFRACTION96.835443038
1.8382-1.91180.1955723310941480.2385479664592753X-RAY DIFFRACTION98.6734693878
1.9118-1.99880.2312472006051480.2235559946052829X-RAY DIFFRACTION99.1011984021
1.9988-2.10410.2241802331411390.2047208722692728X-RAY DIFFRACTION96.8581081081
2.1041-2.2360.2514741197741470.1953666121822782X-RAY DIFFRACTION98.652745032
2.236-2.40860.1812529540351490.1906824640442799X-RAY DIFFRACTION99.1257565568
2.4086-2.6510.2490145565341530.2001061904442797X-RAY DIFFRACTION99.2597577389
2.651-3.03450.2708047805461420.1837710389752775X-RAY DIFFRACTION97.8202548625
3.0345-3.82290.1751895862291500.1773645950662821X-RAY DIFFRACTION99.7649429147
3.8229-47.88870.1884466248911440.1492969427352796X-RAY DIFFRACTION98.8567585743
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)
16.21967787199-7.38929098193-5.359875775052.067056452444.124572055537.246215809340.2180081490361.51131092412-0.180071385476-0.651498565909-0.5972395469290.991530277594-0.874535262945-0.6312594813120.5930739358310.417281171328-0.075585488493-0.1489665434830.393951120660.005888520569940.623953187743-2.334499641928.10567251606-4.5801228465
27.209984209535.532473681872.080574742415.76962324042-0.8388655280368.59407753932-0.01421291686250.459556810736-0.289717445505-0.2506044428450.01213344130910.03562177234940.66705997549-0.2291127169710.05322857952330.270900528950.01838129689940.02775488937870.229442225018-0.06578813145420.23494818519812.42106605465.63350843181-6.90201034826
37.01476636921-3.57709488118-7.007020712913.259258870252.855283270937.782864120930.01546018151250.7975264189110.138421668333-0.139506238664-0.1812423589370.295127205063-0.128345349592-0.4935168919210.06549845879810.1788427274720.00466212159127-0.01400008506660.1860772309450.01112615130410.1992629498579.8364776826713.30031403791.57831099039
49.84652623102-0.919599537407-1.562423567253.6750774421.105526533764.11456912246-0.1617920147770.08030629100280.1515530953890.212659622144-0.1050970728310.8007920932970.031286989458-0.6340287271350.251103149360.198359664158-0.0123016024620.05835093064540.201702019052-0.05556148979250.3480726661562.2973897805216.41482834545.8541829649
56.73614188314-6.256377083665.358217285242.32641032612-1.979722428517.68763995832-0.0941726520419-0.364755745384-0.09441504645690.02231449920570.1170681811070.290253045370.192519809617-0.4798095378560.05059400952010.261557668684-0.06090111387010.03096669232350.231910952752-0.02084418586250.2452850197587.1353710352321.808655507311.5497281067
69.55764435916-1.959161934543.063985484812.10022213625-4.041722128043.95896511818-0.292113855094-0.118344863010.522281172830.7132558495290.2663992707290.419933669628-0.719567144057-0.238348871927-0.04605079768780.3798012589080.005814269312480.1350022498310.33102855578-0.03372965660710.342274153353-1.5243700404522.148833006815.2622896679
72.03394404927-2.965798377681.206639508247.342594843276.886363761728.49380197128-0.00975514988627-0.59545699056-0.1808385490940.827433576537-0.2517724325940.6581650952860.827805547094-0.1933928324280.2018350517240.4049591735410.02415633551470.07045554926290.298928720120.04889876960710.2304625777039.0001853334510.591260553516.6231555694
86.391681041452.648722823313.993511021792.31914412142-0.8606423589562.313133738210.18552550935-0.462979766065-0.6874556429630.528822360083-0.0184654198737-0.05327762134180.5207670422670.0655924096848-0.2907704371640.3610324202790.03591910525980.03955478073770.2891203703260.03803236497570.27123149871912.90405248484.611979165136.07077397603
99.10686556393-5.49536735636-3.004621871666.0801194014.773542308859.71036583699-0.737353243427-0.899907015326-0.2661366060291.028391906620.3025027799810.8445566875310.809921460145-0.444640406090.4094175165510.31947781274-0.02140039361440.1272498757930.321690148220.01115494450420.3690494619670.16128677427111.682041199311.6277326472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 41 )
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 63 )
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 75 )
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 86 )
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 98 )
8X-RAY DIFFRACTION8chain 'A' and (resid 99 through 112 )
9X-RAY DIFFRACTION9chain 'A' and (resid 113 through 122 )

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