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- PDB-5jek: Phosphorylated MAVS in complex with IRF-3 -

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Basic information

Entry
Database: PDB / ID: 5jek
TitlePhosphorylated MAVS in complex with IRF-3
Components
  • Interferon regulatory factor 3
  • MAVS peptide
KeywordsIMMUNE SYSTEM / Innate Immunity / Signaling
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / programmed necrotic cell death / CARD domain binding ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / programmed necrotic cell death / CARD domain binding / TRIF-dependent toll-like receptor signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of cytokine production involved in inflammatory response / cGAS/STING signaling pathway / signal transduction involved in regulation of gene expression / mRNA transcription / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / negative regulation of viral genome replication / DNA-binding transcription activator activity / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / positive regulation of NLRP3 inflammasome complex assembly / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / immune system process / positive regulation of type I interferon production / ubiquitin ligase complex / signaling adaptor activity / positive regulation of defense response to virus by host / antiviral innate immune response / TICAM1-dependent activation of IRF3/IRF7 / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / molecular condensate scaffold activity / mitochondrial membrane / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / cellular response to virus / ISG15 antiviral mechanism / positive regulation of interleukin-6 production / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of protein import into nucleus / Interferon gamma signaling / positive regulation of tumor necrosis factor production / sequence-specific double-stranded DNA binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response / protein-macromolecule adaptor activity / regulation of apoptotic process / molecular adaptor activity / defense response to virus / sequence-specific DNA binding / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / defense response to bacterium / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
IPS1, CARD domain / : / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor ...IPS1, CARD domain / : / Tumour Suppressor Smad4 - #10 / Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily / Caspase recruitment domain / Caspase recruitment domain / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Death-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interferon regulatory factor 3 / Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsZhao, B. / Li, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins.
Authors: Zhao, B. / Shu, C. / Gao, X. / Sankaran, B. / Du, F. / Shelton, C.L. / Herr, A.B. / Ji, J.Y. / Li, P.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon regulatory factor 3
B: Interferon regulatory factor 3
C: MAVS peptide
D: MAVS peptide


Theoretical massNumber of molelcules
Total (without water)57,5654
Polymers57,5654
Non-polymers00
Water1,26170
1
A: Interferon regulatory factor 3
C: MAVS peptide


Theoretical massNumber of molelcules
Total (without water)28,7822
Polymers28,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-10 kcal/mol
Surface area12440 Å2
MethodPISA
2
B: Interferon regulatory factor 3
D: MAVS peptide


Theoretical massNumber of molelcules
Total (without water)28,7822
Polymers28,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-10 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.800, 104.910, 66.270
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon regulatory factor 3 / IRF-3


Mass: 26901.416 Da / Num. of mol.: 2 / Fragment: UNP residues 189-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14653
#2: Protein/peptide MAVS peptide


Mass: 1880.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SER-GLY-CYS-PHE-GLU-ASP-LEU-ALA-ILE-SEP-ALA-SER-THR-SER
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z434*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 5.5, 80 mM MgCl2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→64 Å / Num. obs: 19995 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.4→63.661 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.33
RfactorNum. reflection% reflection
Rfree0.2506 1989 9.96 %
Rwork0.1885 --
obs0.1945 19966 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→63.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 0 70 3968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024006
X-RAY DIFFRACTIONf_angle_d0.6055461
X-RAY DIFFRACTIONf_dihedral_angle_d12.6871439
X-RAY DIFFRACTIONf_chiral_restr0.024584
X-RAY DIFFRACTIONf_plane_restr0.002707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.39261470.31541274X-RAY DIFFRACTION100
2.46-2.52650.35881350.29711272X-RAY DIFFRACTION100
2.5265-2.60090.40111460.27971303X-RAY DIFFRACTION100
2.6009-2.68480.30911380.25961261X-RAY DIFFRACTION100
2.6848-2.78080.34551450.25771308X-RAY DIFFRACTION100
2.7808-2.89210.31111350.23721257X-RAY DIFFRACTION100
2.8921-3.02380.31831460.23131296X-RAY DIFFRACTION100
3.0238-3.18320.28211430.21431277X-RAY DIFFRACTION100
3.1832-3.38260.23781400.20231260X-RAY DIFFRACTION100
3.3826-3.64380.24461400.18791284X-RAY DIFFRACTION100
3.6438-4.01040.21621370.16521297X-RAY DIFFRACTION100
4.0104-4.59060.20491430.1531284X-RAY DIFFRACTION100
4.5906-5.7830.21291450.15421289X-RAY DIFFRACTION100
5.783-63.68330.21711490.15271315X-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)
12.04431.458-0.18928.389-3.08153.79790.1918-0.1609-0.06510.9107-0.3248-0.6453-0.19590.54660.15130.47360.0674-0.09640.4262-0.05910.442731.82111.833910.7563
26.1-1.34410.07418.3461-3.82715.95460.54540.4881-0.658-1.1928-0.664-0.7531.16171.06690.04680.60950.12650.08980.5345-0.08540.596434.24126.7949-0.8974
31.130.0283-0.19454.4248-1.75242.72270.04720.2229-0.1385-0.69040.11070.06420.40070.2295-0.18660.5385-0.0028-0.04230.338-0.07070.399826.476815.2043-3.6327
46.3412-3.9455-0.85994.7965-1.27774.34280.01090.0250.2590.5471-0.0584-0.0478-0.5580.0693-0.06940.774-0.1687-0.08940.30990.01130.531526.291534.2675-3.1101
54.18283.11041.45822.91291.69224.47820.1366-0.21320.7163-0.25-0.37640.5319-0.4501-0.530.30650.38330.08370.01680.4158-0.05340.436836.7995-4.459528.9112
61.3195-1.25570.93378.81880.22663.47750.13460.3661-0.1942-0.4735-0.20710.61610.1188-0.6146-0.03340.4322-0.04160.04930.5295-0.00940.600731.9529-21.364421.2252
76.47553.35451.43417.22381.75553.24260.3119-0.9432-0.08410.965-0.50070.27060.4029-0.40550.21950.65030.01350.1240.5819-0.02890.32637.8336-10.359639.6558
83.46342.5691.43546.83482.15532.61970.0426-0.56830.26950.3477-0.27480.1453-0.1864-0.26450.09790.51850.09320.08820.4592-0.05640.38745.2018-0.846636.6986
97.8804-2.37424.95934.2784-0.90037.20170.9716-0.5803-0.61360.7135-0.1865-1.24232.15790.5-0.56551.12550.3406-0.22650.80430.11421.022738.8048-8.45978.5224
106.3411-0.99357.32870.2957-1.33918.59451.8477-1.0545-0.3317-0.4679-0.18471.29030.7221-0.8419-1.55781.234-0.2390.13780.6910.01661.463822.5144-30.403729.4428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 189 through 285 )
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 317 )
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 382 )
4X-RAY DIFFRACTION4chain 'A' and (resid 383 through 422 )
5X-RAY DIFFRACTION5chain 'B' and (resid 189 through 229 )
6X-RAY DIFFRACTION6chain 'B' and (resid 230 through 267 )
7X-RAY DIFFRACTION7chain 'B' and (resid 268 through 348 )
8X-RAY DIFFRACTION8chain 'B' and (resid 349 through 422 )
9X-RAY DIFFRACTION9chain 'C' and (resid 433 through 446 )
10X-RAY DIFFRACTION10chain 'D' and (resid 435 through 450 )

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