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- PDB-5ms2: Crystal structure of the Legionella pneumophila effector protein ... -

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Basic information

Entry
Database: PDB / ID: 5ms2
TitleCrystal structure of the Legionella pneumophila effector protein RavZ in complex with human LC3B
Components
  • Legionella pneumophila effector protein RavZ
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsHYDROLASE / Autophagy / Host-pathogen interaction
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 / autophagosome assembly / axoneme / 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
Cysteine protease RavZ / Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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: Legionella pneumophila effector protein RavZ
B: Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)63,1032
Polymers63,1032
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-2 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.550, 69.550, 90.170
Angle α, β, γ (deg.)90.00, 101.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Legionella pneumophila effector protein RavZ


Mass: 48523.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg1683 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5ZUV9
#2: 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: 14579.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9GZQ8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.17 M ammonium acetate, 0.085M tri sodium citrate, 25.5% PEG 4000 and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.47→48.08 Å / Num. obs: 22607 / % possible obs: 99.91 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.26 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.51
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.57 / % possible all: 99.42

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQC, 2Z0D

5cqc

2z0d


Resolution: 2.47→48.08 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 23.22
RfactorNum. reflection% reflection
Rfree0.2384 1131 5 %
Rwork0.1774 --
obs0.1805 22607 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.47→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4155 0 0 111 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014251
X-RAY DIFFRACTIONf_angle_d1.4465742
X-RAY DIFFRACTIONf_dihedral_angle_d17.0961608
X-RAY DIFFRACTIONf_chiral_restr0.057648
X-RAY DIFFRACTIONf_plane_restr0.007735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.58240.29861410.24282672X-RAY DIFFRACTION100
2.5824-2.71860.29031390.22832645X-RAY DIFFRACTION100
2.7186-2.88890.29691410.21362679X-RAY DIFFRACTION100
2.8889-3.11190.25871410.1942664X-RAY DIFFRACTION100
3.1119-3.4250.24121400.18022672X-RAY DIFFRACTION100
3.425-3.92040.21851420.15612702X-RAY DIFFRACTION100
3.9204-4.93850.19971410.13932688X-RAY DIFFRACTION100
4.9385-48.0890.22041460.16852754X-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)
17.9846-4.46412.03285.4453-0.7411.25540.33420.097-0.049-0.1296-0.22440.3378-0.131-0.3121-0.10340.22750.05540.09460.22190.01790.225-22.9077-11.8276-10.7976
21.67340.6268-0.99583.0016-1.08762.70650.01560.041-0.2391-0.1327-0.0488-0.24330.09940.0287-0.00990.10380.0443-0.02210.1428-0.00540.2829-6.0867-33.6655-6.2996
32.7109-1.33940.16143.338-0.01710.21650.0660.24060.4963-0.3571-0.1813-0.3059-0.12150.03750.12110.18690.03090.04190.19740.05780.2678-14.7147-1.583-11.1442
46.34170.15724.74164.3623-3.46658.38340.3934-0.7515-0.51250.46670.57680.45841.3091-1.305-0.85110.7773-0.16650.04190.6313-0.0410.3278-41.48790.9958-54.8847
53.12963.56830.24857.0082-1.1121.45250.1255-2.55330.83050.96590.00161.2581-1.5895-2.6877-0.10160.62820.13180.07741.1194-0.02370.4873-44.789411.6881-55.8763
63.49061.74952.54641.50910.02954.3169-0.53570.95270.8238-0.78120.38710.9266-1.4799-1.23230.16261.72261.0043-0.27562.0267-0.12710.8191-49.708116.8835-44.157
75.3628-0.13012.16596.1679-0.6598.5835-0.1097-0.2987-0.1696-0.1213-0.1410.49170.4015-1.82380.21020.71720.06510.05361.01260.10910.3035-38.95711.1673-41.3482
82.97540.7381-2.73944.7865-2.94033.62910.2567-0.32550.0590.4904-0.20130.21220.3661-0.70080.00991.00050.102-0.08650.9988-0.2229-0.0431-39.12132.3509-32.0359
92.0018-2.02313.223.1721-5.31188.9216-0.1217-0.8386-1.31830.2206-0.3048-0.29951.0105-0.24290.35620.98490.1311-0.04870.87170.23060.9676-33.2285-3.5293-33.1511
108.744-7.1564-7.05059.36067.3536.3994-0.64030.55230.92070.5131-0.0455-1.3452-0.3510.42830.62221.48270.6286-0.25191.1797-0.06520.7807-28.627310.096-37.8026
110.52040.11140.20024.4695.72487.3378-0.0149-0.43060.84380.4474-0.0966-0.3636-1.01440.27310.09551.41410.0449-0.35040.7194-0.00760.7317-34.107215.8791-41.5265
125.6638-2.68082.08976.9268-4.58596.7616-0.6213-0.16340.3861-0.51720.0476-0.11520.322-0.92690.48720.87850.1473-0.02750.6058-0.12480.3086-36.26347.4359-47.3682
134.59374.0211-4.4213.5196-3.87024.2573-0.98060.0633-0.9316-1.95370.2694-2.65251.52472.00660.82231.11220.33530.34331.2140.27621.4652-23.8212-3.51-41.732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 275 )
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 429 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 12 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 30 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 70 )
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 83 )
10X-RAY DIFFRACTION10chain 'B' and (resid 84 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 114 )
13X-RAY DIFFRACTION13chain 'B' and (resid 115 through 119 )

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