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- PDB-5f5h: X-ray structure of Roquin ROQ domain in complex with Ox40 hexa-lo... -

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Basic information

Entry
Database: PDB / ID: 5f5h
TitleX-ray structure of Roquin ROQ domain in complex with Ox40 hexa-loop RNA motif
Components
  • RNA (5'-R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)-3')
  • Roquin-1
KeywordsRNA BINDING PROTEIN / ROQ domain / winged-helix domain / Ox40 mRNA
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
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
RNA / RNA (> 10) / Roquin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsJanowski, R. / Schlundt, A. / Sattler, M. / Niessing, D.
CitationJournal: Nat Commun / Year: 2016
Title: Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.
Authors: Janowski, R. / Heinz, G.A. / Schlundt, A. / Wommelsdorf, N. / Brenner, S. / Gruber, A.R. / Blank, M. / Buch, T. / Buhmann, R. / Zavolan, M. / Niessing, D. / Heissmeyer, V. / Sattler, M.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: Roquin-1
C: RNA (5'-R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)-3')
D: RNA (5'-R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1245
Polymers55,0314
Non-polymers921
Water1,78399
1
A: Roquin-1
C: RNA (5'-R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6083
Polymers27,5162
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-22 kcal/mol
Surface area10730 Å2
MethodPISA
2
B: Roquin-1
D: RNA (5'-R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)27,5162
Polymers27,5162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-19 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.660, 115.790, 42.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 20528.561 Da / Num. of mol.: 2 / Fragment: ROQ domain, UNP residues 147-326
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
#2: RNA chain RNA (5'-R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)-3')


Mass: 6987.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, NaCl, Bis-TRIS / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.25363 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25363 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 21018 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.9
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QI0

4qi0


Resolution: 2.23→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 16.735 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25687 1073 4.9 %RANDOM
Rwork0.21635 ---
obs0.2183 21018 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0 Å2
2---2.47 Å20 Å2
3---2.39 Å2
Refinement stepCycle: 1 / Resolution: 2.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 888 6 99 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0173438
X-RAY DIFFRACTIONr_bond_other_d0.0020.022831
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.7524834
X-RAY DIFFRACTIONr_angle_other_deg0.99636555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2385302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36823.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24715466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7971522
X-RAY DIFFRACTIONr_chiral_restr0.0610.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02795
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5273.2641202
X-RAY DIFFRACTIONr_mcbond_other0.5273.2631201
X-RAY DIFFRACTIONr_mcangle_it0.9334.8931500
X-RAY DIFFRACTIONr_mcangle_other0.9334.8941501
X-RAY DIFFRACTIONr_scbond_it0.4993.4052236
X-RAY DIFFRACTIONr_scbond_other0.4983.4052236
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8435.0933333
X-RAY DIFFRACTIONr_long_range_B_refined2.87628.8343976
X-RAY DIFFRACTIONr_long_range_B_other2.85828.7853965
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 86 -
Rwork0.326 1499 -
obs--97.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.87581.21-0.30716.11780.30362.7748-0.0003-0.0635-0.49-0.06780.03450.22450.194-0.1434-0.03420.02580.0184-0.01090.10120.03140.122894.844821.442648.7714
23.1134-0.15160.04216.43960.20632.23190.00450.07550.4969-0.0481-0.0826-0.0036-0.172-0.10410.07810.01650.0257-0.00230.10360.02270.0837119.0241-1.490837.1651
32.3014-2.1445-0.44023.12821.92585.443-0.0317-0.10810.02720.30750.03170.14910.1618-0.303700.1641-0.04550.00080.13560.05650.087796.176725.463466.7752
42.6854-1.1263-0.17341.3158-0.95345.09640.0359-0.24320.1550.242-0.0638-0.3926-0.15670.44050.02790.23870.0106-0.04910.23350.00560.2107120.4123-6.672755.0851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A178 - 325
2X-RAY DIFFRACTION2B174 - 325
3X-RAY DIFFRACTION3C2 - 22
4X-RAY DIFFRACTION4D2 - 22

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