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- PDB-3x1o: Crystal structure of the ROQ domain of human Roquin -

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Basic information

Entry
Database: PDB / ID: 3x1o
TitleCrystal structure of the ROQ domain of human Roquin
ComponentsRoquin-1
KeywordsRNA BINDING PROTEIN / WINGED-HELIX MOTIF / RNA / cytosol
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 / T follicular helper cell differentiation / regulation of T cell receptor signaling pathway / regulation of miRNA metabolic process / 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 / T follicular helper cell differentiation / regulation of T cell receptor signaling pathway / regulation of miRNA metabolic process / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation / 3'-UTR-mediated mRNA destabilization / P-body assembly / miRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / post-transcriptional regulation of gene expression / negative regulation of B cell proliferation / negative regulation of activated T cell proliferation / T cell homeostasis / B cell homeostasis / nuclear-transcribed mRNA catabolic process / 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
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / Roquin II / : / : / Roquin II domain / Roquin 1/2-like, ROQ domain / zinc-RING finger domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / Roquin II / : / : / Roquin II domain / Roquin 1/2-like, ROQ 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Roquin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.201 Å
AuthorsOse, T. / Verma, A. / Cockburn, J.B. / Berrow, N.S. / Alderton, D. / Stuart, D. / Owens, R.J. / Jones, E.Y.
CitationJournal: Nat Commun / Year: 2015
Title: Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis
Authors: Srivastava, M. / Duan, G. / Kershaw, N.J. / Athanasopoulos, V. / Yeo, J.H. / Ose, T. / Hu, D. / Brown, S.H.J. / Jergic, S. / Patel, H.R. / Pratama, A. / Richards, S. / Verma, A. / Jones, E.Y. ...Authors: Srivastava, M. / Duan, G. / Kershaw, N.J. / Athanasopoulos, V. / Yeo, J.H. / Ose, T. / Hu, D. / Brown, S.H.J. / Jergic, S. / Patel, H.R. / Pratama, A. / Richards, S. / Verma, A. / Jones, E.Y. / Heissmeyer, V. / Preiss, T. / Dixon, N.E. / Chong, M.M.W. / Babon, J.J. / Vinuesa, C.G.
History
DepositionNov 26, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Roquin-1
B: Roquin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,21223
Polymers47,5472
Non-polymers2,66521
Water2,990166
1
A: Roquin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,42314
Polymers23,7731
Non-polymers1,65013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Roquin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7899
Polymers23,7731
Non-polymers1,0158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.003, 78.322, 184.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

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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: 23773.301 Da / Num. of mol.: 2 / Fragment: Roq domain, UNP residues 145-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H1, KIAA2025, RNF198 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5TC82
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M lithium chloride, 20% Glycol3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20113 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 8.7 % / Biso Wilson estimate: 25.7 Å2 / Net I/σ(I): 17.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1842 / % possible all: 90.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.201→28.497 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 1216 6.06 %random
Rwork0.2167 ---
obs0.2189 20060 97.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→28.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 21 166 2519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052371
X-RAY DIFFRACTIONf_angle_d0.9283200
X-RAY DIFFRACTIONf_dihedral_angle_d15.833883
X-RAY DIFFRACTIONf_chiral_restr0.035368
X-RAY DIFFRACTIONf_plane_restr0.005408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2006-2.28860.31130.2259192790
2.2886-2.39270.2551210.2271198994
2.3927-2.51880.30911310.2211202395
2.5188-2.67650.30681400.2282206798
2.6765-2.8830.29011300.222212399
2.883-3.17280.23071400.22212134100
3.1728-3.63110.25831690.20562121100
3.6311-4.57170.21581300.19222186100
4.5717-28.49970.23871420.23572274100

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