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

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Basic information

Entry
Database: PDB / ID: 2qfb
TitleCrystal structure of the regulatory domain of human RIG-I with bound Zn
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 / Modulation of host responses by IFN-stimulated genes / 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 / Modulation of host responses by IFN-stimulated genes / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to exogenous dsRNA / RSV-host interactions / response to exogenous dsRNA / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / bicellular tight junction / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / positive regulation of interleukin-6 production / ISG15 antiviral mechanism / response to virus / ruffle membrane / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / actin cytoskeleton / double-stranded RNA binding / TRAF3-dependent IRF activation pathway / double-stranded DNA binding / defense response to virus / gene expression / 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 / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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. ...RIG-I-like receptor, C-terminal regulatory domain / RIG-I, CARD domain repeat 2 / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / 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 domain / DEAD/DEAH box helicase / 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 / MOLECULAR REPLACEMENT / Resolution: 3 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
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)169,18920
Polymers168,53510
Non-polymers65410
Water88349
1
A: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
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)16,9192
Polymers16,8531
Non-polymers651
Water181
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)16,9192
Polymers16,8531
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.900, 76.600, 139.400
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 40897 / Num. obs: 40897 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rsym value: 0.09 / Net I/σ(I): 8.97
Reflection shellResolution: 3→3.18 Å / Redundancy: 2.55 % / Mean I/σ(I) obs: 2.13 / Num. unique all: 5886 / Rsym value: 0.445 / % possible all: 98

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QFD

2qfd


Resolution: 3→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 4111 -RANDOM
Rwork0.248 ---
all0.257 40897 --
obs0.257 40897 98.2 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 10 49 10039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.52
LS refinement shellResolution: 3→3.18 Å / Num. reflection obs: 6606

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