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- PDB-8t5q: SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain -

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Basic information

Entry
Database: PDB / ID: 8t5q
TitleSARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain
Components
  • ORF3a protein
  • TNF receptor-associated factor 2TRAF2
KeywordsSIGNALING PROTEIN/VIRAL PROTEIN / signaling protein-viral protein complex
Function / homology
Function and homology information


host cell lysosome / induction by virus of host reticulophagy / Maturation of protein 3a / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / SARS-CoV-2 modulates autophagy / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex ...host cell lysosome / induction by virus of host reticulophagy / Maturation of protein 3a / CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / SARS-CoV-2 modulates autophagy / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / tumor necrosis factor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / programmed necrotic cell death / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / signal transduction involved in regulation of gene expression / activation of NF-kappaB-inducing kinase activity / mRNA stabilization / vesicle membrane / mitogen-activated protein kinase kinase kinase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / thioesterase binding / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / inorganic cation transmembrane transport / TNFR1-induced proapoptotic signaling / voltage-gated calcium channel complex / RIPK1-mediated regulated necrosis / host cell endoplasmic reticulum / TRAF6 mediated IRF7 activation / non-canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / TRAF6 mediated NF-kB activation / regulation of JNK cascade / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / regulation of protein-containing complex assembly / protein autoubiquitination / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / signaling adaptor activity / ubiquitin ligase complex / positive regulation of JUN kinase activity / voltage-gated potassium channel complex / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / molecular function activator activity / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein catabolic process / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of T cell cytokine production / positive regulation of DNA-binding transcription factor activity / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / protein complex oligomerization / monoatomic ion channel activity / positive regulation of NF-kappaB transcription factor activity / cell cortex / host cell endosome / regulation of apoptotic process / protein phosphatase binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / Attachment and Entry / molecular adaptor activity / host cell endoplasmic reticulum membrane / Ub-specific processing proteases / membrane raft / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / enzyme binding / signal transduction / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / Protein 3a, betacoronavirus / 3a-like viroporin, transmembrane domain, alpha/betacoronavirus / 3a-like viroporin, cytosolic domain, alpha/betacoronavirus / Betacoronavirus viroporin / Coronavirus (CoV) 3a-like viroporin trans-membrane (TM) domain profile. / Coronavirus (CoV) 3a-like viroporin cytosolic (CD) domain profile. ...TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / Protein 3a, betacoronavirus / 3a-like viroporin, transmembrane domain, alpha/betacoronavirus / 3a-like viroporin, cytosolic domain, alpha/betacoronavirus / Betacoronavirus viroporin / Coronavirus (CoV) 3a-like viroporin trans-membrane (TM) domain profile. / Coronavirus (CoV) 3a-like viroporin cytosolic (CD) domain profile. / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / ORF3a protein / TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBusscher, B.M. / Xiao, T.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141350 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127609 United States
CitationJournal: Viruses / Year: 2023
Title: SARS-CoV-2 ORF3a-Mediated NF-kappa B Activation Is Not Dependent on TRAF-Binding Sequence.
Authors: Busscher, B.M. / Befekadu, H.B. / Liu, Z. / Xiao, T.S.
History
DepositionJun 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TNF receptor-associated factor 2
B: TNF receptor-associated factor 2
C: TNF receptor-associated factor 2
D: TNF receptor-associated factor 2
E: TNF receptor-associated factor 2
F: TNF receptor-associated factor 2
G: ORF3a protein
H: ORF3a protein
I: ORF3a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,90617
Polymers128,7049
Non-polymers1,2018
Water5,693316
1
A: TNF receptor-associated factor 2
B: TNF receptor-associated factor 2
C: TNF receptor-associated factor 2
G: ORF3a protein
H: ORF3a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2109
Polymers64,6095
Non-polymers6014
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-30 kcal/mol
Surface area24890 Å2
MethodPISA
2
D: TNF receptor-associated factor 2
E: TNF receptor-associated factor 2
F: TNF receptor-associated factor 2
I: ORF3a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6968
Polymers64,0954
Non-polymers6014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-18 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.200, 84.220, 124.390
Angle α, β, γ (deg.)90.000, 118.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
TNF receptor-associated factor 2 / TRAF2 / E3 ubiquitin-protein ligase TRAF2 / RING-type E3 ubiquitin transferase TRAF2 / Tumor necrosis ...E3 ubiquitin-protein ligase TRAF2 / RING-type E3 ubiquitin transferase TRAF2 / Tumor necrosis factor type 2 receptor-associated protein 3


Mass: 21193.412 Da / Num. of mol.: 6 / Fragment: TRAF domain (UNP residues 315-501)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF2, TRAP3 / Plasmid: pSMT3 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): RIPL / References: UniProt: Q12933
#2: Protein/peptide ORF3a protein / ORF3a / Accessory protein 3a / Protein 3a / Protein U274 / Protein X1


Mass: 514.572 Da / Num. of mol.: 3 / Fragment: UNP residues 36-40 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC3
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium citrate, pH 5.0, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→29.61 Å / Num. obs: 95517 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.62 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rrim(I) all: 0.072 / Net I/σ(I): 12.19
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.49 / Num. unique obs: 7002 / CC1/2: 0.703 / Rpim(I) all: 0.52 / Rrim(I) all: 1 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D01

1d01


Resolution: 1.9→29.61 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.3462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 4757 4.98 %
Rwork0.207 90710 -
obs0.2086 95467 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8109 0 80 316 8505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00748361
X-RAY DIFFRACTIONf_angle_d0.947511266
X-RAY DIFFRACTIONf_chiral_restr0.06381224
X-RAY DIFFRACTIONf_plane_restr0.01031449
X-RAY DIFFRACTIONf_dihedral_angle_d8.88541162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.35571520.32962956X-RAY DIFFRACTION96.91
1.92-1.940.3581430.3063053X-RAY DIFFRACTION99.22
1.94-1.970.34161480.28682990X-RAY DIFFRACTION99.02
1.97-1.990.2941500.27143075X-RAY DIFFRACTION98.71
1.99-2.020.31121690.26312961X-RAY DIFFRACTION99.37
2.02-2.040.2771630.25283068X-RAY DIFFRACTION99.23
2.04-2.070.29551680.24132965X-RAY DIFFRACTION99.33
2.07-2.10.29771430.24343055X-RAY DIFFRACTION98.89
2.1-2.140.31351550.24483004X-RAY DIFFRACTION98.35
2.14-2.170.28341520.2372999X-RAY DIFFRACTION98.32
2.17-2.210.31051740.24473022X-RAY DIFFRACTION98.25
2.21-2.250.28671260.23232958X-RAY DIFFRACTION97.13
2.25-2.290.27711410.23362966X-RAY DIFFRACTION97.52
2.29-2.340.24871850.23223058X-RAY DIFFRACTION99.42
2.34-2.390.28151450.24093007X-RAY DIFFRACTION99.24
2.39-2.450.27761880.23582966X-RAY DIFFRACTION98.9
2.45-2.510.27581670.23863033X-RAY DIFFRACTION98.8
2.51-2.570.27791630.24283051X-RAY DIFFRACTION98.8
2.57-2.650.24721680.23963026X-RAY DIFFRACTION99.29
2.65-2.740.25171620.22213008X-RAY DIFFRACTION99.34
2.74-2.830.23661560.22463066X-RAY DIFFRACTION99.32
2.83-2.950.26661640.22263040X-RAY DIFFRACTION99.53
2.95-3.080.26231650.22083043X-RAY DIFFRACTION98.59
3.08-3.240.22641760.21552917X-RAY DIFFRACTION96.45
3.24-3.450.23811680.19493044X-RAY DIFFRACTION99.07
3.45-3.710.2131500.1843045X-RAY DIFFRACTION99.75
3.71-4.080.19431480.17363091X-RAY DIFFRACTION99.57
4.08-4.670.18211640.15243082X-RAY DIFFRACTION99.21
4.67-5.880.18531520.16593048X-RAY DIFFRACTION98.55
5.88-29.610.21371520.18593113X-RAY DIFFRACTION97.55

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