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- PDB-4ulw: Crystal structure of the ROQ-domain of human ROQUIN1 -

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Basic information

Entry
Database: PDB / ID: 4ulw
TitleCrystal structure of the ROQ-domain of human ROQUIN1
ComponentsROQUIN-1
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN
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 / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation / 3'-UTR-mediated mRNA destabilization ...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 / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation / 3'-UTR-mediated mRNA destabilization / P-body assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / miRNA binding / nuclear-transcribed mRNA catabolic process / 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 / cellular response to interleukin-1 / lymph node development / T cell proliferation / spleen development / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / RNA stem-loop binding / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded RNA binding / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / mRNA binding / RNA binding / zinc ion binding
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.91 Å
AuthorsSchuetz, A. / Heinemann, U.
CitationJournal: Nat.Commun. / Year: 2014
Title: Roquin Binding to Target Mrnas Involves a Winged Helix-Turn- Helix Motif.
Authors: Schuetz, A. / Murakawa, Y. / Rosenbaum, E. / Landthaler, M. / Heinemann, U.
History
DepositionMay 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)34,4942
Polymers34,4942
Non-polymers00
Water2,900161
1
A: ROQUIN-1


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ROQUIN-1


Theoretical massNumber of molelcules
Total (without water)17,2471
Polymers17,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.660, 29.785, 60.197
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2069-

HOH

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Components

#1: Protein ROQUIN-1 / ROQUIN / RING FINGER AND C3H ZINC FINGER PROTEIN 1 / RING FINGER AND CCCH-TYPE ZINC FINGER DOMAIN- ...ROQUIN / RING FINGER AND C3H ZINC FINGER PROTEIN 1 / RING FINGER AND CCCH-TYPE ZINC FINGER DOMAIN-CONTAINING PROTEIN 1 / RING FINGER PROTEIN 198 / RNA-BINDING PROTEIN / RC3H1 PROTEIN


Mass: 17246.844 Da / Num. of mol.: 2 / Fragment: RESIDUES 177-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5TC82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS CRYSTALLISED UNKNOWN DEGRADATION FRAGMENT FROM A PURIFIED PROTEIN THAT ORIGINALLY COMPRISED ...AUTHORS CRYSTALLISED UNKNOWN DEGRADATION FRAGMENT FROM A PURIFIED PROTEIN THAT ORIGINALLY COMPRISED AMINO ACIDS 53-399.

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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: 2.16 Å3/Da / Density % sol: 43.18 % / Description: NONE
Crystal growDetails: 20% (W/V) PEG 6000, 0.2 M LITHIUM CHLORIDE, 0.1 M TRIS/HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→44.39 Å / Num. obs: 23379 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.08
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.01 / % possible all: 95.7

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.91→44.39 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.474 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24144 1169 5 %RANDOM
Rwork0.19997 ---
obs0.20201 22209 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0.98 Å2
2--0.57 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.91→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 0 161 2561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192444
X-RAY DIFFRACTIONr_bond_other_d0.0010.022415
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9693295
X-RAY DIFFRACTIONr_angle_other_deg2.33635545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7325302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91323.571112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93315461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9281522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02565
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_it2.2832.3551208
X-RAY DIFFRACTIONr_mcbond_other2.2742.3551207
X-RAY DIFFRACTIONr_mcangle_it3.2653.5211507
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8912.6831235
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.909→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 81 -
Rwork0.315 1549 -
obs--94.22 %

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