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- PDB-4z30: Crystal structure of the ROQ domain of human Roquin-2 -

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Basic information

Entry
Database: PDB / ID: 4z30
TitleCrystal structure of the ROQ domain of human Roquin-2
ComponentsRoquin-2
KeywordsRNA BINDING PROTEIN / ROQ / RNA-binding / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of miRNA metabolic process / T follicular helper cell differentiation / negative regulation of T-helper 17 cell differentiation / RNA stem-loop binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / limb development / lung alveolus development / T cell homeostasis / B cell homeostasis / lymph node development ...regulation of miRNA metabolic process / T follicular helper cell differentiation / negative regulation of T-helper 17 cell differentiation / RNA stem-loop binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / limb development / lung alveolus development / T cell homeostasis / B cell homeostasis / lymph node development / T cell proliferation / spleen development / post-embryonic development / P-body / multicellular organism growth / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / protein polyubiquitination / positive regulation of non-canonical NF-kappaB signal transduction / ubiquitin protein ligase activity / double-stranded RNA binding / ubiquitin-dependent protein catabolic process / T cell receptor signaling pathway / mRNA binding / intracellular membrane-bounded organelle / cell surface / DNA binding / RNA binding / membrane / metal ion binding
Similarity search - Function
: / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...: / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsDONG, A. / ZHANG, Q. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
CitationJournal: Sci Rep / Year: 2015
Title: New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins.
Authors: Zhang, Q. / Fan, L. / Hou, F. / Dong, A. / Wang, Y.X. / Tong, Y.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roquin-2


Theoretical massNumber of molelcules
Total (without water)36,6765
Polymers36,6761
Non-polymers04
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.764, 144.764, 56.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Roquin-2 / Membrane-associated nucleic acid-binding protein / RING finger and CCCH-type zinc finger domain- ...Membrane-associated nucleic acid-binding protein / RING finger and CCCH-type zinc finger domain-containing protein 2 / RING finger protein 164


Mass: 36676.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H2, MNAB, RNF164 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9HBD1
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.01 Å3/Da / Density % sol: 69.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: mixing 2 uL protein with 1 uL well solution consisting of 3.2 M NaCl, 0.1 M NaOAc pH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 16736 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.028 / Rrim(I) all: 0.088 / Χ2: 1.353 / Net I/av σ(I): 31.742 / Net I/σ(I): 9.8 / Num. measured all: 160955
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.71-2.769.70.9058070.8960.3020.9560.94899.9
2.76-2.819.70.6438410.9750.2160.6791.021100
2.81-2.869.70.5097910.9770.170.5371.004100
2.86-2.929.90.4628180.9780.1530.4871.036100
2.92-2.989.80.348270.990.1130.3581.066100
2.98-3.059.80.2958180.9880.0970.3111.08100
3.05-3.139.80.2998250.9840.0990.3161.137100
3.13-3.219.80.2578270.9890.0850.2711.206100
3.21-3.319.80.198270.9940.0620.21.403100
3.31-3.419.80.1598020.9940.0510.1671.431100
3.41-3.549.70.1378490.9970.0450.1451.402100
3.54-3.689.80.1068160.9980.0340.1121.437100
3.68-3.859.70.0918240.9980.030.0951.435100
3.85-4.059.70.0798480.9980.0260.0831.518100
4.05-4.39.70.0768360.9980.0250.081.688100
4.3-4.639.60.0818420.9970.0270.0852.249100
4.63-5.19.50.0738520.9970.0240.0771.972100
5.1-5.849.40.0658530.9980.0220.0691.462100
5.84-7.359.30.0528820.9990.0170.0551.255100
7.35-508.50.0399510.9990.0140.0411.288100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QIK

4qik


Resolution: 2.71→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU B: 29.251 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.349 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 846 5.1 %RANDOM
Rwork0.2202 ---
obs0.2218 15846 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.31 Å2 / Biso mean: 79.795 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å20 Å2
2--3.28 Å2-0 Å2
3----6.56 Å2
Refinement stepCycle: final / Resolution: 2.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 4 13 2243
Biso mean--30 60.37 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192277
X-RAY DIFFRACTIONr_bond_other_d0.0010.022195
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9633100
X-RAY DIFFRACTIONr_angle_other_deg0.93334993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4115294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7323.43896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.515371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.81519
X-RAY DIFFRACTIONr_chiral_restr0.0740.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
X-RAY DIFFRACTIONr_mcbond_it1.995.7851179
X-RAY DIFFRACTIONr_mcbond_other1.9915.7821178
X-RAY DIFFRACTIONr_mcangle_it3.1958.6681472
LS refinement shellResolution: 2.714→2.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 63 -
Rwork0.362 1157 -
all-1220 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 39.5539 Å / Origin y: -9.4749 Å / Origin z: 1.4 Å
111213212223313233
T0.2804 Å2-0.2733 Å20.042 Å2-0.343 Å2-0.0696 Å2--0.0903 Å2
L1.1447 °20.4513 °2-1.7687 °2-0.2673 °2-0.8177 °2--3.1556 °2
S0.1448 Å °-0.198 Å °0.1598 Å °-0.0013 Å °0.0227 Å °-0.0101 Å °0.1029 Å °-0.0201 Å °-0.1675 Å °

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