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- PDB-5xad: NLIR - LC3B fusion protein -

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Basic information

Entry
Database: PDB / ID: 5xad
TitleNLIR - LC3B fusion protein
Components
  • Microtubule-associated proteins 1A/1B light chain 3B
  • Uncharacterised protein
KeywordsPROTEIN BINDING / Autophagy / LC3 / Atg8 / fusion protein
Function / homology
Function and homology information


host intracellular membrane-bounded organelle / protein delipidation / SARS-CoV-2 modulates autophagy / ceramide binding / symbiont-mediated suppression of host autophagy / phosphatidylinositol-3-phosphate binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation ...host intracellular membrane-bounded organelle / protein delipidation / SARS-CoV-2 modulates autophagy / ceramide binding / symbiont-mediated suppression of host autophagy / phosphatidylinositol-3-phosphate 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 / cysteine-type peptidase activity / autophagosome / Pexophagy / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / mitochondrial membrane / host cell cytoplasmic vesicle membrane / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / microtubule binding / cytoplasmic vesicle / microtubule / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / ubiquitin protein ligase binding / mitochondrion / proteolysis / extracellular region / membrane / cytosol
Similarity search - Function
: / RavZ C-terminal PI3P-binding domain / RavZ catalytic domain / 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
Dot/Icm T4SS effector RavZ / Cysteine protease RavZ / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsKwon, D.H. / Kim, L. / Song, H.K.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: A novel conformation of the LC3-interacting region motif revealed by the structure of a complex between LC3B and RavZ
Authors: Kwon, D.H. / Kim, L. / Kim, B.W. / Kim, J.H. / Roh, K.H. / Choi, E.J. / Song, H.K.
History
DepositionMar 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Uncharacterised protein
D: Uncharacterised protein


Theoretical massNumber of molelcules
Total (without water)33,6684
Polymers33,6684
Non-polymers00
Water3,585199
1
A: Microtubule-associated proteins 1A/1B light chain 3B
C: Uncharacterised protein


Theoretical massNumber of molelcules
Total (without water)16,8342
Polymers16,8342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Uncharacterised protein


Theoretical massNumber of molelcules
Total (without water)16,8342
Polymers16,8342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.735, 65.735, 127.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 14019.088 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 BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9GZQ8
#2: Protein/peptide Uncharacterised protein


Mass: 2814.870 Da / Num. of mol.: 2 / Fragment: UNP residues 12-34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A129J378, UniProt: Q5ZUV9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.0 M Ammonium sulfate, 100mM CHES/NaOH pH 9.5, 200mM NaCl.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→37.5 Å / Num. obs: 23313 / % possible obs: 99.5 % / Redundancy: 8.8 % / Net I/σ(I): 50.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VTU

3vtu


Resolution: 1.88→35.6 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.28
RfactorNum. reflection% reflection
Rfree0.2525 2000 8.58 %
Rwork0.2091 --
obs0.2128 23313 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 0 199 2546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082386
X-RAY DIFFRACTIONf_angle_d1.2063208
X-RAY DIFFRACTIONf_dihedral_angle_d11.4721475
X-RAY DIFFRACTIONf_chiral_restr0.06355
X-RAY DIFFRACTIONf_plane_restr0.007420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8795-1.92650.37931390.26781485X-RAY DIFFRACTION99
1.9265-1.97860.32081390.25081475X-RAY DIFFRACTION99
1.9786-2.03680.271390.23051488X-RAY DIFFRACTION100
2.0368-2.10260.30921410.23491499X-RAY DIFFRACTION100
2.1026-2.17770.23251400.22091489X-RAY DIFFRACTION100
2.1777-2.26490.25651420.22431521X-RAY DIFFRACTION100
2.2649-2.36790.31141410.21621503X-RAY DIFFRACTION100
2.3679-2.49280.29881430.22071512X-RAY DIFFRACTION100
2.4928-2.64890.28711440.2181536X-RAY DIFFRACTION100
2.6489-2.85340.26811420.22061520X-RAY DIFFRACTION100
2.8534-3.14040.24091440.21541530X-RAY DIFFRACTION100
3.1404-3.59450.23911460.19891561X-RAY DIFFRACTION100
3.5945-4.52740.2141470.17571568X-RAY DIFFRACTION100
4.5274-37.51880.23591530.20991626X-RAY DIFFRACTION96
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)
10.9429-1.8294-0.55186.90731.66460.7831-0.4766-0.46280.01761.0574-0.41810.3862-1.6077-0.91740.01820.7310.25780.02250.43780.04650.3835117.9798117.1288135.4594
23.55130.28091.58951.3061-0.4653.6175-0.16740.20970.08490.03360.09030.0317-0.1861-0.1077-0.07190.1892-0.01550.01720.1621-0.00840.1953130.4008111.081124.9062
32.1568-0.86070.81123.0926-0.7854.4181-0.1739-0.3283-0.01180.41740.21290.0796-0.757-0.2307-0.00030.27770.08560.02220.19840.00490.2041135.4692112.6534140.4907
44.3079-1.4927-0.20611.4384-1.65793.06010.0624-0.29780.02860.1270.33010.0341-0.301-0.3774-0.03550.30480.09220.03450.25070.06140.2834136.1043106.0322144.7326
53.0536-0.48791.05311.6672-0.83023.8311-0.0204-0.1988-0.35950.0320.26190.16930.1943-0.0723-0.20910.1957-0.01530.02380.19470.04140.27132.7501103.3101134.4298
66.54564.532-9.08888.0981-5.51631.9996-1.1676-0.3737-0.4209-0.1041-0.2557-1.43850.2860.0008-2.35460.55390.0734-0.19990.4125-0.14141.0556145.125774.129134.8985
72.47741.1557-0.7035.35862.42985.0738-0.10150.2214-0.14070.35130.4975-1.6134-0.24720.98380.04650.16250.05540.06810.2797-0.05360.608139.773581.188131.0829
88.08211.43690.2555.44090.41425.0343-0.2540.00330.6393-0.81160.0460.2687-0.2654-0.4124-0.03950.2658-0.02730.00150.22870.03040.3988128.132285.5153129.0096
93.96740.42182.02513.53650.68693.59240.3186-0.5212-0.16820.3759-0.1168-0.38910.49780.0275-0.11210.3055-0.063-0.03210.2833-0.03850.398132.015576.3855143.2879
105.4197-0.15490.07546.82591.17156.78380.079-0.8389-0.13630.78070.49050.31711.0965-0.25520.00290.5079-0.1347-0.0590.4031-0.02140.3388127.869173.2714151.4202
114.7274-0.6233-0.33524.86361.91044.31920.1189-0.7302-0.15510.26370.018-0.3370.43940.0438-0.11310.5785-0.0976-0.04270.58650.03040.3728133.421479.1072153.917
124.72520.9097-0.61784.3046-0.05566.24240.1016-0.52470.57820.13280.0495-0.02890.1615-0.2999-0.03870.3019-0.0251-0.00160.2785-0.04890.405128.785389.3357141.7913
135.8629-0.56291.94970.28460.18431.17920.1204-0.9799-0.44320.15760.2889-0.10460.4683-0.3117-0.45990.3659-0.0321-0.04870.369-0.03450.4517139.978178.8685150.9155
145.0869-3.4933.84192.438-2.49653.15760.2903-0.00240.0378-0.8068-0.2184-0.17360.40740.4611-0.02620.27120.0530.03030.32890.00240.1915120.3614129.7811127.9179
158.1255-0.3971-1.89015.40914.31124.4330.15560.80783.73-1.71110.30260.1861-1.4860.5989-0.07720.5242-0.1740.05850.66850.13280.8609121.9956145.5091120.5184
164.02481.3523-0.7852.0133-6.02469.05820.33370.26-0.0841-0.2604-0.5359-0.45930.31421.24810.07380.3385-0.1034-0.07990.3913-0.01030.2525121.8276132.9326130.778
171.3481-1.145-2.72131.62292.62475.58880.06640.03180.14060.3714-0.0423-0.15710.3958-0.0117-0.1420.3961-0.08780.00420.26610.00340.3369139.638565.7945124.9076
182.55961.9180.48673.78111.24242.1788-0.36220.5721-0.4038-0.461-0.03320.1677-0.1732-0.33890.04110.3944-0.06890.01420.4767-0.00360.3612134.800452.5791113.0012
194.10842.33231.7763.39623.56653.98550.4170.35040.61130.81790.5214-0.3067-0.0395-0.04970.40340.3828-0.0170.03490.2816-0.03060.3632139.057461.3812125.9984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 118 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 6 )
7X-RAY DIFFRACTION7chain 'B' and (resid 7 through 12 )
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 70 )
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 94 )
12X-RAY DIFFRACTION12chain 'B' and (resid 95 through 108 )
13X-RAY DIFFRACTION13chain 'B' and (resid 109 through 120 )
14X-RAY DIFFRACTION14chain 'C' and (resid 11 through 17 )
15X-RAY DIFFRACTION15chain 'C' and (resid 18 through 28 )
16X-RAY DIFFRACTION16chain 'C' and (resid 29 through 34 )
17X-RAY DIFFRACTION17chain 'D' and (resid 10 through 17 )
18X-RAY DIFFRACTION18chain 'D' and (resid 18 through 28 )
19X-RAY DIFFRACTION19chain 'D' and (resid 29 through 34 )

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