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- PDB-8t5p: SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain -

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Basic information

Entry
Database: PDB / ID: 8t5p
TitleSARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain
Components
  • ORF3a protein
  • TNF receptor-associated factor 3
KeywordsSIGNALING PROTEIN/VIRAL PROTEIN / signaling protein-viral protein complex
Function / homology
Function and homology information


host cell lysosome / symbiont-mediated activation of host reticulophagy / Maturation of protein 3a / regulation of interferon-beta production / TRAF3 deficiency - HSE / SARS-CoV-2 modulates autophagy / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus ...host cell lysosome / symbiont-mediated activation of host reticulophagy / Maturation of protein 3a / regulation of interferon-beta production / TRAF3 deficiency - HSE / SARS-CoV-2 modulates autophagy / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / inorganic cation transmembrane transport / voltage-gated calcium channel complex / host cell endoplasmic reticulum / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / monoatomic ion channel activity / regulation of proteolysis / positive regulation of type I interferon production / ubiquitin ligase complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / tumor necrosis factor-mediated signaling pathway / signaling adaptor activity / voltage-gated potassium channel complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / regulation of cytokine production / molecular function activator activity / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / host cell endosome / protein phosphatase binding / regulation of apoptotic process / defense response to virus / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / Attachment and Entry / cell surface receptor signaling pathway / endosome / endosome membrane / host cell endoplasmic reticulum membrane / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / signal transduction / mitochondrion / extracellular region / zinc ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / 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 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / 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. / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ORF3a protein / TNF receptor-associated factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 3
B: TNF receptor-associated factor 3
C: TNF receptor-associated factor 3
D: TNF receptor-associated factor 3
E: TNF receptor-associated factor 3
F: TNF receptor-associated factor 3
G: ORF3a protein
H: ORF3a protein
I: ORF3a protein


Theoretical massNumber of molelcules
Total (without water)132,5439
Polymers132,5439
Non-polymers00
Water48627
1
A: TNF receptor-associated factor 3
B: TNF receptor-associated factor 3
C: TNF receptor-associated factor 3
G: ORF3a protein
H: ORF3a protein


Theoretical massNumber of molelcules
Total (without water)66,5295
Polymers66,5295
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-47 kcal/mol
Surface area27950 Å2
MethodPISA
2
D: TNF receptor-associated factor 3
E: TNF receptor-associated factor 3
F: TNF receptor-associated factor 3
I: ORF3a protein


Theoretical massNumber of molelcules
Total (without water)66,0144
Polymers66,0144
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-46 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.350, 83.750, 83.800
Angle α, β, γ (deg.)60.030, 79.260, 83.800
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
TNF receptor-associated factor 3 / CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein ...CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein 1 / LAP1 / RING-type E3 ubiquitin transferase TRAF3


Mass: 21833.135 Da / Num. of mol.: 6 / Fragment: TRAF domain (UNP residues 377-568)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3, CAP-1, CRAF1, TRAFAMN / Plasmid: pSMT3 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): RIPL / References: UniProt: Q13114
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 13% PEG3350, 0.1 M Tris, pH 8.0, 0.25 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→41.77 Å / Num. obs: 64645 / % possible obs: 97.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 55.89 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.065 / Rrim(I) all: 0.174 / Net I/σ(I): 11.11
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.72 / Num. unique obs: 4608 / CC1/2: 0.505 / Rpim(I) all: 0.928 / Rrim(I) all: 2.329 / % possible all: 94.3

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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 4GHU

4ghu


Resolution: 2.5→41.77 Å / SU ML: 0.432 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 30.4071
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 3087 4.78 %
Rwork0.1969 61540 -
obs0.1991 64627 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.56 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9201 0 0 27 9228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819405
X-RAY DIFFRACTIONf_angle_d0.924912678
X-RAY DIFFRACTIONf_chiral_restr0.05231380
X-RAY DIFFRACTIONf_plane_restr0.00791611
X-RAY DIFFRACTIONf_dihedral_angle_d5.95781260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.44761630.40342668X-RAY DIFFRACTION93.19
2.54-2.580.51261470.37842735X-RAY DIFFRACTION96.94
2.58-2.620.36121540.35242772X-RAY DIFFRACTION97.37
2.62-2.670.41571580.33512747X-RAY DIFFRACTION96.45
2.67-2.720.35091620.30582733X-RAY DIFFRACTION97.28
2.72-2.780.30891200.26912825X-RAY DIFFRACTION97.42
2.78-2.840.28741200.23852816X-RAY DIFFRACTION97.74
2.84-2.90.31541290.24372825X-RAY DIFFRACTION97.62
2.9-2.980.33461320.26842763X-RAY DIFFRACTION97.57
2.98-3.060.37791580.26622763X-RAY DIFFRACTION98.09
3.06-3.150.30671440.26572841X-RAY DIFFRACTION98.42
3.15-3.250.30621570.23242786X-RAY DIFFRACTION98.4
3.25-3.360.22321300.20742835X-RAY DIFFRACTION98.11
3.37-3.50.27191350.19952807X-RAY DIFFRACTION98.43
3.5-3.660.26621510.20212810X-RAY DIFFRACTION98.7
3.66-3.850.21851450.18572805X-RAY DIFFRACTION98.7
3.85-4.090.20141170.17132851X-RAY DIFFRACTION98.8
4.09-4.410.2021580.15212854X-RAY DIFFRACTION98.95
4.41-4.850.18411150.14192813X-RAY DIFFRACTION98.55
4.85-5.550.16641110.13782893X-RAY DIFFRACTION98.75
5.55-6.990.1821170.18832829X-RAY DIFFRACTION99.06
6.99-41.770.1831640.15762769X-RAY DIFFRACTION98

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