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- PDB-8t2n: Crystal structure of GABARAP in complex with the LIR of NSs3 -

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Basic information

Entry
Database: PDB / ID: 8t2n
TitleCrystal structure of GABARAP in complex with the LIR of NSs3
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Non-structural protein S
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 / positive regulation of protein K48-linked ubiquitination / suppression by virus of host type I interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / 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 / positive regulation of protein K48-linked ubiquitination / suppression by virus of host type I interferon production / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / negative stranded viral RNA replication / phosphatidylethanolamine binding / protein serine/threonine kinase inhibitor activity / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / sperm midpiece / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / symbiont-mediated suppression of host gene expression / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / host cell cytoplasm / lysosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / Golgi membrane / ubiquitin protein ligase binding / synapse / host cell nucleus / plasma membrane / 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
Gamma-aminobutyric acid receptor-associated protein / Non-structural protein S
Similarity search - Component
Biological speciesHomo sapiens (human)
Rift Valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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: Gamma-aminobutyric acid receptor-associated protein
B: Non-structural protein S
C: Gamma-aminobutyric acid receptor-associated protein
D: Non-structural protein S


Theoretical massNumber of molelcules
Total (without water)33,5644
Polymers33,5644
Non-polymers00
Water79344
1
A: Gamma-aminobutyric acid receptor-associated protein
B: Non-structural protein S


Theoretical massNumber of molelcules
Total (without water)16,7822
Polymers16,7822
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area7590 Å2
MethodPISA
2
C: Gamma-aminobutyric acid receptor-associated protein
D: Non-structural protein S


Theoretical massNumber of molelcules
Total (without water)16,7822
Polymers16,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-9 kcal/mol
Surface area8420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.725, 31.485, 68.917
Angle α, β, γ (deg.)90.00, 115.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 14086.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95166
#2: Protein/peptide Non-structural protein S / NSs


Mass: 2695.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift Valley fever virus / Gene: NSS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21698
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.88→36.74 Å / Num. obs: 20163 / % possible obs: 88.41 % / Redundancy: 5.5 % / CC1/2: 0.9999 / Net I/σ(I): 14.13
Reflection shellResolution: 1.88→1.947 Å / Num. unique obs: 833 / CC1/2: 0.105

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→36.74 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1958 9.92 %
Rwork0.2205 --
obs0.2248 19739 88.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 0 44 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022253
X-RAY DIFFRACTIONf_angle_d0.5573044
X-RAY DIFFRACTIONf_dihedral_angle_d12.169866
X-RAY DIFFRACTIONf_chiral_restr0.049315
X-RAY DIFFRACTIONf_plane_restr0.004392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.920.4867640.4452469X-RAY DIFFRACTION34
1.93-1.980.427770.4202702X-RAY DIFFRACTION49
1.98-2.040.42981030.4021928X-RAY DIFFRACTION66
2.04-2.10.41631260.36091286X-RAY DIFFRACTION88
2.1-2.180.3751480.33561361X-RAY DIFFRACTION97
2.18-2.260.32951700.29811421X-RAY DIFFRACTION100
2.26-2.370.32311460.27871434X-RAY DIFFRACTION100
2.37-2.490.31021610.26391412X-RAY DIFFRACTION100
2.49-2.650.29331590.2521450X-RAY DIFFRACTION100
2.65-2.850.31731470.27041449X-RAY DIFFRACTION100
2.85-3.140.29181650.2621447X-RAY DIFFRACTION100
3.14-3.590.2871580.21931440X-RAY DIFFRACTION100
3.59-4.520.21951650.18231457X-RAY DIFFRACTION100
4.52-36.740.22031690.17931525X-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)
14.6805-0.20530.38681.3635-0.31173.5685-0.25170.98540.1817-0.44680.02930.3431-0.5124-0.4859-0.01080.59880.0026-0.00180.49180.01870.4558-12.792-11.89046.1885
20.9213-1.2290.54292.00340.13362.63230.1105-0.00130.4072-0.1637-0.0673-0.6405-0.46430.379-0.00090.4808-0.00080.0460.43460.05710.5448-3.1464-12.774418.1649
31.0056-0.92220.06421.22620.47191.23580.11480.3764-0.37350.1135-0.25790.79840.5515-0.79790.02290.66020.01710.08240.5335-0.03640.6673-15.328-17.556911.5026
40.3427-0.36820.09820.4-0.13610.2345-0.4699-0.09671.03430.2940.38191.3767-0.8518-1.06390.00751.0193-0.16530.12060.9486-0.24680.9956-11.2878-6.323526.1485
50.53270.61371.1050.70831.27582.2961-0.2239-0.1834-0.64670.34890.2389-0.76740.98320.94570.03480.8802-0.02530.19941.17120.17810.8848-0.8366-16.5443.4049
61.53980.5979-0.56080.2775-0.41042.00330.13131.5382-0.2088-0.9835-0.39160.33530.5228-0.2122-0.00830.7154-0.0626-0.15751.0039-0.08970.6927-35.0356-16.30889.9902
72.5078-0.92841.80371.6611-0.49166.14340.0313-0.0612-0.01470.08870.19320.4410.0245-0.63250.00010.3927-0.0149-0.00610.4021-0.01520.4929-34.1802-13.246125.6767
80.06160.01650.00160.1122-0.16030.2393-0.41120.0911-0.1201-0.84780.6210.5830.2518-0.579-0.00010.72010.0217-0.17311.3971-0.02881.1066-45.8674-15.006216.7484
90.2103-0.2487-0.14320.28810.16920.09690.0427-1.17690.08511.09470.1046-0.7201-0.14850.1721-0.00221.16410.1929-0.07631.801-0.09621.3288-47.9604-0.574439.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 116 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 43 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 24 )
7X-RAY DIFFRACTION7chain 'C' and (resid 25 through 117 )
8X-RAY DIFFRACTION8chain 'D' and (resid 33 through 37 )
9X-RAY DIFFRACTION9chain 'D' and (resid 38 through 49 )

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