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- PDB-3eqt: Crystal structure of human LGP2 C-terminal domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 3eqt
TitleCrystal structure of human LGP2 C-terminal domain in complex with dsRNA
Components
  • 5'-R(*GP*CP*GP*CP*GP*CP*GP*C)-3'
  • ATP-dependent RNA helicase DHX58
KeywordsRNA BINDING PROTEIN/RNA / innate immunity / RIG-I-like helicases / viral RNA detection / LGP2-dsRNA complex / ATP-binding / Coiled coil / Cytoplasm / Helicase / Hydrolase / Immune response / Nucleotide-binding / Polymorphism / RNA-binding / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / positive regulation of RIG-I signaling pathway / negative regulation of type I interferon production / regulation of innate immune response / cytoplasmic pattern recognition receptor signaling pathway / antiviral innate immune response / positive regulation of type I interferon production / negative regulation of innate immune response ...positive regulation of MDA-5 signaling pathway / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / positive regulation of RIG-I signaling pathway / negative regulation of type I interferon production / regulation of innate immune response / cytoplasmic pattern recognition receptor signaling pathway / antiviral innate immune response / positive regulation of type I interferon production / negative regulation of innate immune response / response to bacterium / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / double-stranded RNA binding / RNA helicase activity / single-stranded RNA binding / RNA helicase / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
RIG-I-like receptor, C-terminal regulatory domain / 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. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit ...RIG-I-like receptor, C-terminal regulatory domain / 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. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 / ATP-dependent RNA helicase DHX58
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, P. / Li, X.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The RIG-I-like Receptor LGP2 Recognizes the Termini of Double-stranded RNA
Authors: Li, X. / Ranjith-Kumar, C.T. / Brooks, M.T. / Dharmaiah, S. / Herr, A.B. / Kao, C. / Li, P.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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 / _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_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: ATP-dependent RNA helicase DHX58
B: ATP-dependent RNA helicase DHX58
C: 5'-R(*GP*CP*GP*CP*GP*CP*GP*C)-3'
D: 5'-R(*GP*CP*GP*CP*GP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6826
Polymers38,5524
Non-polymers1312
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.458, 54.191, 67.203
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ATP-dependent RNA helicase DHX58 / Probable ATP-dependent helicase LGP2 / Protein D11Lgp2 homolog


Mass: 16719.178 Da / Num. of mol.: 2 / Fragment: LGP2 C-terminal domain (UNP residues 541 to 678)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: D11LGP2E, DHX58, LGP2 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96C10, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: RNA chain 5'-R(*GP*CP*GP*CP*GP*CP*GP*C)-3'


Mass: 2556.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized RNA
#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 / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium sulfate, 16-18% PEG3350, 0.1 M Tris-HCl buffer, protein concentration 30 mg/ml, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
10.2 M ammonium sulfate11
2PEG335011
30.2 M ammonium sulfate12
4PEG335012

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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: May 26, 2008 / Details: Osmic High Flux
RadiationMonochromator: Osmic High Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 28240 / Num. obs: 28126 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 0.462
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2769 / Rsym value: 0.336 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2QFB

2qfb


Resolution: 2→50 Å / Cross valid method: Rfree, throghout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1309 -random
Rwork0.213 ---
obs0.214 27234 96.4 %-
all-28299 --
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 338 2 215 2721
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.008
X-RAY DIFFRACTIONc_bond_d1.43
LS refinement shellResolution: 2→2.03 Å
RfactorNum. reflection% reflection
Rfree0.41 47 -
Rwork0.315 --
obs-825 98 %

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