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- PDB-2w4r: Crystal structure of the regulatory domain of human LGP2 -

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Basic information

Entry
Database: PDB / ID: 2w4r
TitleCrystal structure of the regulatory domain of human LGP2
ComponentsPROBABLE ATP-DEPENDENT RNA HELICASE DHX58
KeywordsHYDROLASE / INNATE IMMUNITY / IMMUNE RESPONSE / NUCLEOTIDE-BINDING / COILED COIL / ATP-BINDING / POLYMORPHISM / DOUBLE-STRAND RNA BINDING PROTEIN / HELICASE / CYTOPLASM / RNA-BINDING
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
: / ATP-dependent RNA helicase DHX58
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPippig, D.A. / Hellmuth, J.C. / Cui, S. / Kirchhofer, A. / Lammens, K. / Lammens, A. / Schmidt, A. / Rothenfusser, S. / Hopfner, K.P.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The Regulatory Domain of the Rig-I Family ATPase Lgp2 Senses Double-Stranded RNA.
Authors: Pippig, D.A. / Hellmuth, J.C. / Cui, S. / Kirchhofer, A. / Lammens, K. / Lammens, A. / Schmidt, A. / Rothenfusser, S. / Hopfner, K.P.
History
DepositionDec 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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

Downloads & links

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Assembly

Deposited unit
A: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
B: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
C: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
D: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,13713
Polymers64,8554
Non-polymers1,2839
Water2,306128
1
A: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5103
Polymers16,2141
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5103
Polymers16,2141
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6064
Polymers16,2141
Non-polymers3933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PROBABLE ATP-DEPENDENT RNA HELICASE DHX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5103
Polymers16,2141
Non-polymers2972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.670, 75.620, 147.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PROBABLE ATP-DEPENDENT RNA HELICASE DHX58 / PROBABLE ATP-DEPENDENT HELICASE LGP2 / PROTEIN D11LGP2 HOMOLOG / LGP2


Mass: 16213.653 Da / Num. of mol.: 4 / Fragment: REGULATORY DOMAIN, RESIDUES 537-678
Source method: isolated from a genetically manipulated source
Details: 4 HG PER ASU 5 SO4 PER ASU / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA
References: UniProt: Q96C10, 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.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.78 Å3/Da / Density % sol: 55.8 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.009
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 39540 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 44.01 Å2 / Rsym value: 0.06 / Net I/σ(I): 13.68
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.58 / Rsym value: 0.29 / % possible all: 85.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QFD

2qfd


Resolution: 2.6→48.7 Å / SU ML: 0.43 / σ(F): 1.96 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1088 4.8 %
Rwork0.214 --
obs0.217 22410 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.89 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 43.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.2345 Å20 Å2-0 Å2
2--6.3261 Å2-0 Å2
3----8.5607 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 29 128 4182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064158
X-RAY DIFFRACTIONf_angle_d1.0055629
X-RAY DIFFRACTIONf_dihedral_angle_d19.741524
X-RAY DIFFRACTIONf_chiral_restr0.069601
X-RAY DIFFRACTIONf_plane_restr0.005724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5958-2.71390.34731250.26722574X-RAY DIFFRACTION97
2.7139-2.8570.34411100.25242678X-RAY DIFFRACTION100
2.857-3.0360.3171390.25052666X-RAY DIFFRACTION100
3.036-3.27030.30231410.22892651X-RAY DIFFRACTION100
3.2703-3.59940.27831400.21232669X-RAY DIFFRACTION99
3.5994-4.120.2211430.17982611X-RAY DIFFRACTION97
4.12-5.18980.23661370.16662697X-RAY DIFFRACTION98
5.1898-48.71360.24211530.22592776X-RAY DIFFRACTION97

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