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- PDB-3lrr: Crystal structure of human RIG-I CTD bound to a 12 bp AU rich 5' ... -

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Basic information

Entry
Database: PDB / ID: 3lrr
TitleCrystal structure of human RIG-I CTD bound to a 12 bp AU rich 5' ppp dsRNA
Components
  • Probable ATP-dependent RNA helicase DDX58
  • RNA (5'-R(*(ATP)P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*U)-3')
KeywordsHYDROLASE/RNA / Innate immunity / viral RNA / RIG-I like receptors / Antiviral defense / ATP-binding / Helicase / Hydrolase / Immune response / Metal-binding / Nucleotide-binding / RNA-binding / HYDROLASE-RNA 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 / cellular response to exogenous dsRNA / 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 / positive regulation of tumor necrosis factor production / double-stranded RNA binding / gene expression / TRAF3-dependent IRF activation pathway / 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 / 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
RNA / RNA (> 10) / Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLi, P.
CitationJournal: Structure / Year: 2010
Title: The Structural Basis of 5' Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain.
Authors: Lu, C. / Xu, H. / Ranjith-Kumar, C.T. / Brooks, M.T. / Hou, T.Y. / Hu, F. / Herr, A.B. / Strong, R.K. / Kao, C.C. / Li, P.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
C: RNA (5'-R(*(ATP)P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*U)-3')
D: RNA (5'-R(*(ATP)P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3926
Polymers36,2614
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.010, 83.010, 111.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsAuthors state that the asymmetric unit contains a 2:1 complex of human RIG-I CTD bound to a 12 bp dsRNA

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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 / Retinoic acid-inducible gene ...DEAD-box protein 58 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 14203.516 Da / Num. of mol.: 2 / Fragment: RIG-I CTD (UNP residues 803 to 923)
Source method: isolated from a genetically manipulated source
Details: C-terminal Histag / Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58, RIG-I / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O95786, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: RNA chain RNA (5'-R(*(ATP)P*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*U)-3')


Mass: 3927.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: In vitro transcribed RNA with T7 RNA polymerase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3,350 (15%) plus ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 174 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2009 / Details: Osmic
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 23670 / Num. obs: 22092 / % possible obs: 93.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 36
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2119 / Rsym value: 0.457 / % possible all: 90.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Free RIG-I CTD, pdb ID. 2QFB chain A

2qfb


Resolution: 2.15→30.19 Å / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Refined with CNS 1.1 again twinned data. Twin fraction, 0.478
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1407 -Random
Rwork0.187 ---
all0.187 23670 --
obs0.187 20357 91.8 %-
Refinement stepCycle: LAST / Resolution: 2.15→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 522 2 0 2522
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.54
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellHighest resolution: 2.15 Å
RfactorNum. reflection% reflection
Rfree0.228 1407 -
Rwork0.187 --
obs-20357 86 %

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