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- PDB-4qi0: X-ray structure of the ROQ domain from murine Roquin-1 -

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Basic information

Entry
Database: PDB / ID: 4qi0
TitleX-ray structure of the ROQ domain from murine Roquin-1
ComponentsRoquin-1
KeywordsRNA BINDING PROTEIN / ROQ domain / winged-helix domain / RNA binding / Tnf CDE RNA
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsJanowski, R. / Schlundt, A. / Sattler, M. / Niessing, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation.
Authors: Schlundt, A. / Heinz, G.A. / Janowski, R. / Geerlof, A. / Stehle, R. / Heissmeyer, V. / Niessing, D. / Sattler, M.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,1193
Polymers41,0572
Non-polymers621
Water5,819323
1
A: Roquin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5912
Polymers20,5291
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Roquin-1


Theoretical massNumber of molelcules
Total (without water)20,5291
Polymers20,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.220, 79.510, 184.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-471-

HOH

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gm551, Kiaa2025, Rc3h1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q4VGL6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 300 mM Na Tartrate, 100 mM Bis-Tris-Propane, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.90745 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 26, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.90745 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 30555 / Num. obs: 30555 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.7
Reflection shellResolution: 1.94→1.99 Å / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
Auto-Rickshawphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.94→92.46 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.092 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.131 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20556 1251 4.1 %RANDOM
Rwork0.16141 ---
obs0.16327 29304 99.85 %-
all-29304 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20 Å2
2--0.13 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.94→92.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 4 323 2842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192714
X-RAY DIFFRACTIONr_bond_other_d0.0010.022689
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9713694
X-RAY DIFFRACTIONr_angle_other_deg0.94436209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49424.211133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9681524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_mcbond_it1.6331.3771308
X-RAY DIFFRACTIONr_mcbond_other1.6331.3751307
X-RAY DIFFRACTIONr_mcangle_it2.522.0421644
X-RAY DIFFRACTIONr_mcangle_other2.5192.0461645
X-RAY DIFFRACTIONr_scbond_it2.081.6871405
X-RAY DIFFRACTIONr_scbond_other2.081.6881405
X-RAY DIFFRACTIONr_scangle_other3.3892.4332026
X-RAY DIFFRACTIONr_long_range_B_refined6.95712.3423319
X-RAY DIFFRACTIONr_long_range_B_other6.69711.5393178
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 88 -
Rwork0.308 2123 -
obs--99.82 %
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)
10.53790.04520.11620.69470.27281.46720.03770.027-0.05090.0402-0.00830.00440.01460.0053-0.02940.0214-0.00340.00430.0392-0.00540.0406-19.597-14.5175.586
20.28310.53650.43651.91661.3911.3054-0.0282-0.02650.0369-0.00290.00130.0981-0.051-0.01260.02690.1136-0.0056-0.02690.0727-0.00280.0239-13.3096.51637.47
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A174 - 326
2X-RAY DIFFRACTION2B165 - 326

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