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- PDB-4ywq: Crystal structure of the ROQ domain of human Roquin-1 -

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Basic information

Entry
Database: PDB / ID: 4ywq
TitleCrystal structure of the ROQ domain of human Roquin-1
ComponentsRoquin-1
KeywordsRNA BINDING PROTEIN / ROQ / RNA binding domain / E3 ubiquitin ligase / Structural Genomics / Structural Genomics Consortium / SGC / transcription
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 / RNA stem-loop binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / miRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 / lymph node development / cellular response to interleukin-1 / T cell proliferation / spleen development / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / protein polyubiquitination / positive regulation of non-canonical NF-kappaB signal transduction / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded RNA binding / ubiquitin-dependent protein catabolic process / T cell receptor signaling pathway / mRNA binding / RNA binding / zinc ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / : / 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. ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / : / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDong, A. / Zhang, Q. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the ROQ domain of human Roquin-1
Authors: Zhang, Q. / Dong, A. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,48018
Polymers39,0222
Non-polymers45916
Water3,279182
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-78 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.205, 29.560, 59.926
Angle α, β, γ (deg.)90.000, 101.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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: 19510.771 Da / Num. of mol.: 2 / Fragment: ROQ domain (UNP residues 159-328)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H1, KIAA2025, RNF198 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q5TC82

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Non-polymers , 6 types, 198 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein mixed with elastase at 1:1000 (w/w) ratio right before crystallization, 25% PEG8000, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionRedundancy: 4.8 % / Number: 157706 / Rmerge(I) obs: 0.125 / Χ2: 2.32 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 32886 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.615010.0855.9594.7
3.664.6110.0794.6844.6
3.23.6610.0954.7644.7
2.913.210.1124.124.8
2.72.9110.1283.3974.9
2.542.710.142.8814.9
2.412.5410.1562.6044.9
2.312.4110.1662.3174.9
2.222.3110.182.1134.9
2.142.2210.1961.8065
2.072.1410.2211.7144.9
2.022.0710.2511.5414.9
1.962.0210.2751.3874.9
1.911.9610.3181.2424.9
1.871.9110.4161.0644.9
1.831.8710.4740.9984.8
1.791.8310.5570.8784.7
1.761.7910.5870.8444.6
1.731.7610.7010.8594.5
1.71.7310.7290.7794.3
ReflectionResolution: 1.7→50 Å / Num. obs: 32886 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.063 / Rrim(I) all: 0.14 / Χ2: 2.32 / Net I/av σ(I): 22.571 / Net I/σ(I): 7.1 / Num. measured all: 157706
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.30.72916380.6420.3890.8290.77999.9
1.73-1.764.50.70116300.6830.3660.7930.85999.8
1.76-1.794.60.58716200.7740.2990.660.84499.9
1.79-1.834.70.55716310.8110.2810.6250.878100
1.83-1.874.80.47416410.8360.2390.5320.99899.9
1.87-1.914.90.41616210.8790.2070.4661.064100
1.91-1.964.90.31816580.9250.1590.3561.242100
1.96-2.024.90.27516020.9390.1370.3081.38799.8
2.02-2.074.90.25116400.9470.1250.2811.54199.9
2.07-2.144.90.22116410.940.1110.2481.71499.9
2.14-2.2250.19616450.9610.0970.2191.80699.9
2.22-2.314.90.1816400.9560.090.2022.113100
2.31-2.414.90.16616300.9670.0830.1862.31799.8
2.41-2.544.90.15616390.9710.0770.1742.60499.8
2.54-2.74.90.1416580.9770.0690.1572.88199.9
2.7-2.914.90.12816670.980.0630.1433.39799.8
2.91-3.24.80.11216340.9820.0560.1254.1299.8
3.2-3.664.70.09516730.9860.0480.1074.76499.1
3.66-4.614.60.07916610.990.040.0894.68498.8
4.61-504.70.08517170.990.0430.0965.95997.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.625 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 849 2.6 %RANDOM
Rwork0.1988 ---
obs0.1998 32036 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.26 Å2 / Biso mean: 21.714 Å2 / Biso min: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å2-0 Å2-0.29 Å2
2---0.6 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 27 184 2570
Biso mean--32.34 31.61 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192554
X-RAY DIFFRACTIONr_bond_other_d0.0020.022534
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9853473
X-RAY DIFFRACTIONr_angle_other_deg0.91635825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2045342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10523.214112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88115450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4291524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
X-RAY DIFFRACTIONr_mcbond_it1.1672.0691262
X-RAY DIFFRACTIONr_mcbond_other1.1662.0691260
X-RAY DIFFRACTIONr_mcangle_it1.8913.091588
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 55 -
Rwork0.257 2216 -
all-2271 -
obs--92.85 %

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