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- PDB-6tqb: X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE1 ... -

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Basic information

Entry
Database: PDB / ID: 6tqb
TitleX-ray structure of Roquin ROQ domain in complex with a UCP3 CDE1 SL RNA motif
Components
  • RNA (5'-R(P*GP*GP*AP*AP*AP*UP*UP*AP*UP*AP*UP*UP*AP*AP*UP*UP*UP*CP*C)-3')
  • Roquin-1
KeywordsRNA BINDING PROTEIN / roquin / ROQ domain / RNA binding / UCP1
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 / negative regulation of T-helper 17 cell differentiation / positive regulation of mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / T follicular helper cell differentiation ...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 / negative regulation of T-helper 17 cell differentiation / positive regulation of mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / T follicular helper cell differentiation / regulation of germinal center formation / miRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated 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 / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / RNA stem-loop binding / protein polyubiquitination / cytoplasmic stress granule / ubiquitin-protein transferase activity / T cell receptor signaling pathway / double-stranded RNA binding / regulation of gene expression / mRNA binding / zinc ion binding / cytoplasm
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
RNA / RNA (> 10) / Roquin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBinas, O. / Tants, J.-N. / Peter, S.A. / Janowski, R. / Davydova, E. / Braun, J. / Niessing, D. / Schwalbe, H. / Weigand, J.E. / Schlundt, A.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis for the recognition of transiently structured AU-rich elements by Roquin.
Authors: Binas, O. / Tants, J.N. / Peter, S.A. / Janowski, R. / Davydova, E. / Braun, J. / Niessing, D. / Schwalbe, H. / Weigand, J.E. / Schlundt, A.
History
DepositionDec 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: RNA (5'-R(P*GP*GP*AP*AP*AP*UP*UP*AP*UP*AP*UP*UP*AP*AP*UP*UP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,05213
Polymers26,5382
Non-polymers51411
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-59 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.990, 86.990, 72.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-858-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#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: 20528.561 Da / Num. of mol.: 1
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)
References: UniProt: Q4VGL6, RING-type E3 ubiquitin transferase
#2: RNA chain RNA (5'-R(P*GP*GP*AP*AP*AP*UP*UP*AP*UP*AP*UP*UP*AP*AP*UP*UP*UP*CP*C)-3')


Mass: 6009.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 5 types, 252 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Bis Tris Propane pH 6.5, 0.29 M Sodium Tartrate, 19 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36355 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.16
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2053 / CC1/2: 0.797 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QI2

4qi2


Resolution: 1.6→47.08 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.482 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 1760 4.8 %RANDOM
Rwork0.1563 ---
obs0.1582 34595 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.37 Å2 / Biso mean: 28.248 Å2 / Biso min: 16.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: final / Resolution: 1.6→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 400 31 255 1911
Biso mean--44.61 43.76 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122033
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181584
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.5162887
X-RAY DIFFRACTIONr_angle_other_deg1.5971.8263727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.52421.79578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2921512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021872
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02426
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 93 -
Rwork0.238 1959 -
all-2052 -
obs--75.41 %

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