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- PDB-3og8: Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended... -

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Basic information

Entry
Database: PDB / ID: 3og8
TitleCrystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA
Components
  • Antiviral innate immune response receptor RIG-I
  • RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
KeywordsHYDROLASE/RNA / Innate immunity / viral RNA sensing / RNA binding domain / IPS-1 / cytosolic / 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 / 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-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)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, P.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5' triphosphate.
Authors: Lu, C. / Ranjith-Kumar, C.T. / Hao, L. / Kao, C.C. / Li, P.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _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

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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: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
D: RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2396
Polymers39,1084
Non-polymers1312
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-27 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.990, 70.300, 125.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsRIG-I CTD / dsRNA

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Components

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


Mass: 15046.478 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: C829S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIGI, DDX58 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95786, RNA helicase
#2: RNA chain RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Mass: 4507.755 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27% PEG MME 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 1, 2010 / Details: osmic
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.4→35.96 Å / Num. all: 13440 / Num. obs: 13384 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 29.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1316 / Rsym value: 0.448 / % possible all: 98

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35.96 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 1329 random
Rwork0.217 --
obs0.217 12860 -
all-13440 -
Refinement stepCycle: LAST / Resolution: 2.4→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 596 2 133 2829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.32

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