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- PDB-5ms5: Low-salt structure of RavZ LIR2-fused human LC3B -

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Basic information

Entry
Database: PDB / ID: 5ms5
TitleLow-salt structure of RavZ LIR2-fused human LC3B
ComponentsRavZ,Microtubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / Autophagy / Host-pathogen interaction / Protein binding /RavZ / LIR / LC3
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 / Pexophagy / autophagosome / 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 / cytoplasmic vesicle / microtubule binding / 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
Cysteine protease RavZ / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPantoom, S. / Vetter, I.R. / Wu, Y.W.
CitationJournal: Elife / Year: 2017
Title: Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins.
Authors: Yang, A. / Pantoom, S. / Wu, Y.W.
History
DepositionDec 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,4137
Polymers31,9362
Non-polymers4765
Water3,567198
1
A: RavZ,Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2524
Polymers15,9681
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RavZ,Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1603
Polymers15,9681
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.610, 69.610, 117.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

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Components

#1: Protein RavZ,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: 15968.087 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The fusion protein of RavZ LIR (RESIDUES 25-36) and Microtubule-associated proteins 1A/1B light chain 3B (RESIDUES 2-119)
Source: (gene. exp.) Legionella pneumophila (bacteria), (gene. exp.) Homo sapiens (human)
Gene: lpg1683, MAP1LC3B, MAP1ALC3 / Plasmid: pMAL / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5ZUV9, UniProt: Q9GZQ8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citric acid anhydrous and 1.6 M ammonium sulfate
PH range: 3.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 1.53→49.222 Å / Num. obs: 44250 / % possible obs: 100 % / Redundancy: 25.4 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1769 / Net I/σ(I): 14.69
Reflection shellResolution: 1.53→1.585 Å / Redundancy: 24.6 % / Rmerge(I) obs: 2.205 / Mean I/σ(I) obs: 1.42 / CC1/2: 0.165 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z0E

2z0e


Resolution: 1.53→49.222 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 2214 5 %
Rwork0.2078 --
obs0.2096 44237 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→49.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 26 198 2323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082169
X-RAY DIFFRACTIONf_angle_d1.1792921
X-RAY DIFFRACTIONf_dihedral_angle_d11.846846
X-RAY DIFFRACTIONf_chiral_restr0.056323
X-RAY DIFFRACTIONf_plane_restr0.007375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.56330.39971360.41952573X-RAY DIFFRACTION100
1.5633-1.59960.39671360.38652583X-RAY DIFFRACTION100
1.5996-1.63960.36141370.36522599X-RAY DIFFRACTION100
1.6396-1.6840.35811340.33972563X-RAY DIFFRACTION100
1.684-1.73350.36831370.32732596X-RAY DIFFRACTION100
1.7335-1.78950.38431350.30432592X-RAY DIFFRACTION100
1.7895-1.85340.31821360.27892584X-RAY DIFFRACTION100
1.8534-1.92770.26531370.2352602X-RAY DIFFRACTION100
1.9277-2.01540.27011370.21572598X-RAY DIFFRACTION100
2.0154-2.12160.26881380.19842609X-RAY DIFFRACTION100
2.1216-2.25460.23111380.18452625X-RAY DIFFRACTION100
2.2546-2.42870.23181380.17862622X-RAY DIFFRACTION100
2.4287-2.6730.22251410.19582656X-RAY DIFFRACTION100
2.673-3.05980.23271400.1922654X-RAY DIFFRACTION100
3.0598-3.85480.19911420.17242703X-RAY DIFFRACTION100
3.8548-49.24720.19931520.17092864X-RAY DIFFRACTION100
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)
11.5277-3.0003-2.82527.63044.2346.3379-0.13710.2404-0.43210.00330.4373-0.211-0.1869-0.183-0.13640.22320.0770.05030.19180.06730.20148.1472-20.7854-29.5397
21.8315-0.81791.53121.5809-1.44345.401-0.00290.15230.0585-0.1743-0.0821-0.03370.13450.22140.08150.1047-0.03370.00260.1662-0.00730.182145.24398.6205-7.7626
34.37933.8220.93133.3110.82630.2488-0.00050.49-0.71950.47890.2468-0.93730.46950.5413-0.23040.6610.170.10330.5552-0.040.368323.2139-38.4371-11.4014
48.6336-6.10883.94017.6095-3.87365.3013-0.06740.2555-0.381-0.3896-0.12320.32630.6154-0.13150.1380.3425-0.06630.07230.1482-0.03610.203223.9109-13.0855-22.2376
52.28620.5925-0.83583.2797-1.1255.8030.0126-0.20370.05270.08960.018-0.0347-0.10840.169-0.02420.1119-0.0067-0.01470.1079-0.02670.175920.1117-2.2351-6.957
64.9015-0.2969-2.33547.4647-0.43013.7257-0.0845-0.25810.0423-0.10670.0294-0.2844-0.09120.69330.06570.0776-0.01140.00340.1135-0.00590.185427.2513-5.5794-9.1786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -16 through 4 )
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 117 )
3X-RAY DIFFRACTION3chain 'B' and (resid -12 through 6 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 26 )
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 102 )
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 118 )

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