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- PDB-8t2l: Crystal structure of LC3A in complex with the LIR of NSs4 -

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Basic information

Entry
Database: PDB / ID: 8t2l
TitleCrystal structure of LC3A in complex with the LIR of NSs4
ComponentsNon-structural protein S,Microtubule-associated proteins 1A/1B light chain 3A chimera
KeywordsPROTEIN BINDING / Rift Valley fever virus / autophagy / LC3 / GABARAP / LIR
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / symbiont-mediated suppression of host transcription / cellular response to oxygen-glucose deprivation / suppression by virus of host type I interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / negative stranded viral RNA replication / phosphatidylethanolamine binding ...symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / symbiont-mediated suppression of host transcription / cellular response to oxygen-glucose deprivation / suppression by virus of host type I interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / negative stranded viral RNA replication / phosphatidylethanolamine binding / protein serine/threonine kinase inhibitor activity / 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 / symbiont-mediated suppression of host gene expression / microtubule binding / microtubule / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / host cell nucleus / cytosol
Similarity search - Function
Phlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Non-structural protein S / Microtubule-associated proteins 1A/1B light chain 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsAli, M.G.H. / Wahba, H.M. / Cyr, N. / Omichinski, J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA) United States
CitationJournal: Plos Pathog. / Year: 2024
Title: An LIR motif in the Rift Valley fever virus NSs protein is critical for the interaction with LC3 family members and inhibition of autophagy.
Authors: Petraccione, K. / Ali, M.G.H. / Cyr, N. / Wahba, H.M. / Stocker, T. / Akhrymuk, M. / Akhrymuk, I. / Panny, L. / Bracci, N. / Cafaro, R. / Sastre, D. / Silberfarb, A. / O'Maille, P. / ...Authors: Petraccione, K. / Ali, M.G.H. / Cyr, N. / Wahba, H.M. / Stocker, T. / Akhrymuk, M. / Akhrymuk, I. / Panny, L. / Bracci, N. / Cafaro, R. / Sastre, D. / Silberfarb, A. / O'Maille, P. / Omichinski, J. / Kehn-Hall, K.
History
DepositionJun 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein S,Microtubule-associated proteins 1A/1B light chain 3A chimera
B: Non-structural protein S,Microtubule-associated proteins 1A/1B light chain 3A chimera


Theoretical massNumber of molelcules
Total (without water)30,8592
Polymers30,8592
Non-polymers00
Water1,00956
1
A: Non-structural protein S,Microtubule-associated proteins 1A/1B light chain 3A chimera


Theoretical massNumber of molelcules
Total (without water)15,4301
Polymers15,4301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein S,Microtubule-associated proteins 1A/1B light chain 3A chimera


Theoretical massNumber of molelcules
Total (without water)15,4301
Polymers15,4301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.995, 50.267, 137.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-structural protein S,Microtubule-associated proteins 1A/1B light chain 3A chimera / NSs / Autophagy-related protein LC3 A / Autophagy-related ubiquitin-like modifier LC3 A / MAP1 ...NSs / 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: 15429.536 Da / Num. of mol.: 2
Fragment: GS is the remain of the removed expression tag. The N terminus of Nss has been fused with Q9H492 to facilitate the crystalization.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSS, MAP1LC3A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21698, UniProt: Q9H492
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.2M Na-citrate, 5% Isopropanol, 0.1M MES buffer PH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 2.24→32.6 Å / Num. obs: 12899 / % possible obs: 93.28 % / Redundancy: 6.2 % / CC1/2: 0.997 / Net I/σ(I): 10.9
Reflection shellResolution: 2.24→2.32 Å / Num. unique obs: 1072 / CC1/2: 0.747

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→32.6 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 1217 10.03 %
Rwork0.2308 --
obs0.2354 12135 93.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 56 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022139
X-RAY DIFFRACTIONf_angle_d0.5272885
X-RAY DIFFRACTIONf_dihedral_angle_d11.638843
X-RAY DIFFRACTIONf_chiral_restr0.023313
X-RAY DIFFRACTIONf_plane_restr0.003380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.32950.36781180.30271075X-RAY DIFFRACTION85
2.3295-2.43550.35171180.28711102X-RAY DIFFRACTION87
2.4355-2.56390.32791260.29091142X-RAY DIFFRACTION89
2.5639-2.72440.30691330.26821177X-RAY DIFFRACTION93
2.7244-2.93470.27941370.25451211X-RAY DIFFRACTION94
2.9347-3.22980.3161390.25341245X-RAY DIFFRACTION97
3.2298-3.69670.30861440.23371287X-RAY DIFFRACTION97
3.6967-4.65550.2311470.1981305X-RAY DIFFRACTION99
4.6555-32.60.23941550.20071374X-RAY DIFFRACTION98
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)
13.70870.3718-0.06271.13410.3893.2617-0.4003-0.01280.1752-0.52010.2102-0.286-0.6461-0.15140.08780.53720.062-0.07260.3354-0.00730.2543-11.1795-25.38399.0249
22.74510.20050.94672.6706-0.05211.5416-0.05670.05640.0192-0.01510.073-0.1026-0.14720.0436-0.02920.20450.0180.07290.2648-0.01660.2848-6.6295-8.933233.6577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B
2X-RAY DIFFRACTION2chain A

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