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- PDB-4txa: Crystal structure of N-terminus of Roquin -

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Basic information

Entry
Database: PDB / ID: 4txa
TitleCrystal structure of N-terminus of Roquin
ComponentsRoquin-1
KeywordsRNA BINDING PROTEIN / RNA-binding HEPN RING ROQ
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 / positive regulation of mRNA catabolic process / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation ...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 / positive regulation of mRNA catabolic process / 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 / miRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / 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 / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / regulation of gene expression / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / RING-type zinc-finger / 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 / RING-type zinc-finger / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKershaw, N.J. / Vinuesa, C.G. / Babon, J.J.
CitationJournal: To Be Published
Title: N/A
Authors: kershaw, N.J.
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roquin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3853
Polymers54,2541
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.804, 80.191, 54.858
Angle α, β, γ (deg.)90.00, 111.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Roquin-1 / Roquin / Protein Sanroque / RING finger and C3H zinc finger protein 1 / RING finger and CCCH-type ...Roquin / Protein Sanroque / RING finger and C3H zinc finger protein 1 / RING finger and CCCH-type zinc finger domain-containing protein 1


Mass: 54254.219 Da / Num. of mol.: 1 / Fragment: UNP residues 1-484 / Mutation: M199R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rc3h1, Gm551, Kiaa2025 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q4VGL6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 7-20% PEG 8000, 0.1M CHES / PH range: 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.265102 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.265102 Å / Relative weight: 1
ReflectionResolution: 2.75→68.71 Å / Num. obs: 14921 / % possible obs: 98.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 91.79 Å2 / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassificationNB
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→37.83 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 728 4.9 %
Rwork0.2184 --
obs0.2201 14761 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→37.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 2 0 2838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042886
X-RAY DIFFRACTIONf_angle_d0.9663919
X-RAY DIFFRACTIONf_dihedral_angle_d11.8371073
X-RAY DIFFRACTIONf_chiral_restr0.073464
X-RAY DIFFRACTIONf_plane_restr0.004505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.84830.3925890.38881947X-RAY DIFFRACTION69
2.8483-2.96230.43351420.3752609X-RAY DIFFRACTION94
2.9623-3.0970.39151490.36552755X-RAY DIFFRACTION98
3.097-3.26020.34821370.30922774X-RAY DIFFRACTION98
3.2602-3.46440.34711460.27312763X-RAY DIFFRACTION98
3.4644-3.73160.27131430.24942765X-RAY DIFFRACTION99
3.7316-4.10680.25551370.20722779X-RAY DIFFRACTION99
4.1068-4.70010.21681560.18572754X-RAY DIFFRACTION99
4.7001-5.91790.23861440.21022788X-RAY DIFFRACTION99
5.9179-37.83390.19521320.17362777X-RAY DIFFRACTION99

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