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- PDB-7mk1: Structure of a protein-modified aptamer complex -

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Basic information

Entry
Database: PDB / ID: 7mk1
TitleStructure of a protein-modified aptamer complex
Components
  • Antiviral innate immune response receptor RIG-I
  • DNA (41-MER)
KeywordsIMMUNE SYSTEM/DNA / innate immunity / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation ...regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / RSV-host interactions / cellular response to exogenous dsRNA / response to exogenous dsRNA / TRAF6 mediated NF-kB activation / antiviral innate immune response / bicellular tight junction / positive regulation of interferon-alpha production / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Ovarian tumor domain proteases / actin cytoskeleton / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily ...RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRen, X. / Pyle, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA.
Authors: Ren, X. / Gelinas, A.D. / Linehan, M. / Iwasaki, A. / Wang, W. / Janjic, N. / Pyle, A.M.
History
DepositionApr 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antiviral innate immune response receptor RIG-I
B: Antiviral innate immune response receptor RIG-I
C: DNA (41-MER)
D: DNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5818
Polymers59,4024
Non-polymers1794
Water7,530418
1
A: Antiviral innate immune response receptor RIG-I
C: DNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7914
Polymers29,7012
Non-polymers902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-22 kcal/mol
Surface area12430 Å2
MethodPISA
2
B: Antiviral innate immune response receptor RIG-I
D: DNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7914
Polymers29,7012
Non-polymers902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-21 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.126, 86.632, 87.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Antiviral innate immune response receptor RIG-I / DEAD box protein 58 / Probable ATP-dependent RNA helicase DDX58 / RIG-I-like receptor 1 / RLR-1 / ...DEAD box protein 58 / Probable ATP-dependent RNA helicase DDX58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 14648.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli (E. coli) / References: UniProt: O95786, RNA helicase
#2: DNA chain DNA (41-MER)


Mass: 15052.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3350, 0.01 M Na acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→57.75 Å / Num. obs: 46578 / % possible obs: 99.76 % / Redundancy: 2 % / Biso Wilson estimate: 47.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0304 / Rpim(I) all: 0.0304 / Rrim(I) all: 0.043 / Net I/σ(I): 10.72
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Num. unique obs: 4608 / CC1/2: 0.549 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OG8
Resolution: 1.9→57.75 Å / SU ML: 0.2666 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.7527 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 2324 4.99 %
Rwork0.1884 44264 -
obs0.1901 46588 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 2036 4 418 4454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01954320
X-RAY DIFFRACTIONf_angle_d4.33156102
X-RAY DIFFRACTIONf_chiral_restr0.4229584
X-RAY DIFFRACTIONf_plane_restr0.0122460
X-RAY DIFFRACTIONf_dihedral_angle_d36.07471480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.38131090.37352609X-RAY DIFFRACTION99.96
1.94-1.980.32861212573X-RAY DIFFRACTION99.93
1.98-2.030.29011392566X-RAY DIFFRACTION99.89
2.03-2.080.3141190.29712596X-RAY DIFFRACTION99.85
2.08-2.130.3311320.27042561X-RAY DIFFRACTION99.74
2.13-2.20.30641530.25542573X-RAY DIFFRACTION99.96
2.2-2.270.26141270.24262576X-RAY DIFFRACTION99.82
2.27-2.350.28061400.21652577X-RAY DIFFRACTION100
2.35-2.440.29011280.22692580X-RAY DIFFRACTION99.93
2.44-2.550.28791370.20772614X-RAY DIFFRACTION99.93
2.55-2.690.31871420.21342588X-RAY DIFFRACTION99.82
2.69-2.860.26071230.20592626X-RAY DIFFRACTION99.85
2.86-3.080.23721430.19822591X-RAY DIFFRACTION99.35
3.08-3.390.22211470.1762590X-RAY DIFFRACTION99.53
3.39-3.880.20561420.16292647X-RAY DIFFRACTION99.71
3.88-4.880.14941600.13842636X-RAY DIFFRACTION99.57

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