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- PDB-4qik: Crystal structure of the ROQ domain of human Roquin in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4qik
TitleCrystal structure of the ROQ domain of human Roquin in complex with the TNF23 RNA duplex
Components
  • 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'
  • Roquin-1
KeywordsRNA BINDING PROTEIN/RNA / RNA duplex / Winged-helix motif / mRNA secondary structure / mRNA decay / immune responses / autoimmunity / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


negative regulation of germinal center formation / negative regulation of T-helper cell differentiation / regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CCR4-NOT complex binding / regulation of T cell receptor signaling pathway / regulation of miRNA metabolic process / T follicular helper cell differentiation / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation / 3'-UTR-mediated mRNA destabilization ...negative regulation of germinal center formation / negative regulation of T-helper cell differentiation / regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CCR4-NOT complex binding / regulation of T cell receptor signaling pathway / regulation of miRNA metabolic process / T follicular helper cell differentiation / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation / 3'-UTR-mediated mRNA destabilization / P-body assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / miRNA binding / nuclear-transcribed mRNA catabolic process / post-transcriptional regulation of gene expression / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / cellular response to interleukin-1 / lymph node development / T cell proliferation / spleen development / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / RNA stem-loop binding / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded RNA binding / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / mRNA binding / RNA binding / zinc ion binding
Similarity search - Function
: / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Zinc finger, RING-type, conserved site ...: / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RNA / RNA (> 10) / Roquin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTan, D. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA.
Authors: Tan, D. / Zhou, M. / Kiledjian, M. / Tong, L.
History
DepositionMay 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Roquin-1
B: Roquin-1
C: 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'
D: 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,45319
Polymers89,8644
Non-polymers58815
Water15,943885
1
A: Roquin-1
C: 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'
D: 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,60511
Polymers52,3223
Non-polymers2848
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Roquin-1
C: 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'
D: 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,62610
Polymers52,3223
Non-polymers3057
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-152 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.800, 93.100, 100.200
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 Roquin-1 / Roquin / RING finger and C3H zinc finger protein 1 / RING finger and CCCH-type zinc finger domain- ...Roquin / RING finger and C3H zinc finger protein 1 / RING finger and CCCH-type zinc finger domain-containing protein 1 / RING finger protein 198


Mass: 37542.695 Da / Num. of mol.: 2 / Fragment: ROQ domain (UNP residues 88-407)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H1, KIAA2025, RNF198 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TC82
#2: RNA chain 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3'


Mass: 7389.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TNF23 double-stranded RNA
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 885 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.1 M sodium citrate/citric acid buffer, pH 5.7, 1.5 M lithium chloride, 18%-21% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2013
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 129493 / Num. obs: 129493 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.682 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6371 4.94 %RANDOM
Rwork0.1774 ---
obs0.1791 128927 99.69 %-
all-128927 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4741 767 20 885 6413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115737
X-RAY DIFFRACTIONf_angle_d1.2097950
X-RAY DIFFRACTIONf_dihedral_angle_d13.7722303
X-RAY DIFFRACTIONf_chiral_restr0.077941
X-RAY DIFFRACTIONf_plane_restr0.006898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.26526500.226612267X-RAY DIFFRACTION100
1.9679-2.04670.23816160.198912346X-RAY DIFFRACTION100
2.0467-2.13980.22986170.182412288X-RAY DIFFRACTION100
2.1398-2.25260.21156160.17512360X-RAY DIFFRACTION100
2.2526-2.39380.22746640.174412228X-RAY DIFFRACTION100
2.3938-2.57860.21286040.17412358X-RAY DIFFRACTION100
2.5786-2.8380.21046920.187812218X-RAY DIFFRACTION100
2.838-3.24850.23626620.186312275X-RAY DIFFRACTION100
3.2485-4.09210.19066060.159912265X-RAY DIFFRACTION100
4.0921-39.69030.19166440.171511951X-RAY DIFFRACTION97

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