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- PDB-2qfd: Crystal structure of the regulatory domain of human RIG-I with bo... -

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Basic information

Entry
Database: PDB / ID: 2qfd
TitleCrystal structure of the regulatory domain of human RIG-I with bound Hg
ComponentsProbable ATP-dependent RNA helicase DDX58
KeywordsHYDROLASE / Zinc Finger / Alternative splicing / Antiviral defense / ATP-binding / Helicase / Immune response / Innate immunity / Interferon induction / Nucleotide-binding / Polymorphism / RNA-binding / Ubl conjugation
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 / response to exogenous dsRNA / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / bicellular tight junction / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / actin cytoskeleton / double-stranded RNA binding / positive regulation of tumor necrosis factor production / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / RNA helicase / Ub-specific processing proteases / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / GTP binding / positive regulation of gene expression / 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 / cytosol / cytoplasm
Similarity search - Function
RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 ...RIG-I-like receptor, C-terminal regulatory domain / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 / Beta Complex / 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 / Mainly Beta
Similarity search - Domain/homology
: / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsCui, S. / Lammens, A. / Lammens, K. / Hopfner, K.P.
CitationJournal: Mol.Cell / Year: 2008
Title: The C-Terminal Regulatory Domain Is the RNA 5'-Triphosphate Sensor of RIG-I.
Authors: Cui, S. / Eisenacher, K. / Kirchhofer, A. / Brzozka, K. / Lammens, A. / Lammens, K. / Fujita, T. / Conzelmann, K.K. / Krug, A. / Hopfner, K.P.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
C: Probable ATP-dependent RNA helicase DDX58
D: Probable ATP-dependent RNA helicase DDX58
E: Probable ATP-dependent RNA helicase DDX58
F: Probable ATP-dependent RNA helicase DDX58
G: Probable ATP-dependent RNA helicase DDX58
H: Probable ATP-dependent RNA helicase DDX58
I: Probable ATP-dependent RNA helicase DDX58
J: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,54120
Polymers168,53510
Non-polymers2,00610
Water1,838102
1
A: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0542
Polymers16,8531
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.150, 76.540, 137.900
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer

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Components

#1: Protein
Probable ATP-dependent RNA helicase DDX58 / DEAD-box protein 58 / Retinoic acid-inducible gene 1 protein / RIG-1 / RIG-I


Mass: 16853.498 Da / Num. of mol.: 10 / Fragment: Regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta
References: UniProt: O95786, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 0.1 M CHES pH 10.0, 18% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00800, 1.00900, 1.01000
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
21.0091
31.011
ReflectionResolution: 2.7→50 Å / Num. all: 106277 / Num. obs: 106277 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.88 % / Rsym value: 0.067 / Net I/σ(I): 14.36
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 3.76 % / Mean I/σ(I) obs: 3.04 / Num. unique all: 16547 / Rsym value: 0.438 / % possible all: 94.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 5535 -RANDOM
Rwork0.241 ---
all0.253 54390 --
obs0.253 54390 97.6 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 10 102 10092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.49
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2.7→2.87 Å

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