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- PDB-6tqa: X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE2 ... -

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Basic information

Entry
Database: PDB / ID: 6tqa
TitleX-ray structure of Roquin ROQ domain in complex with a UCP3 CDE2 SL RNA motif
Components
  • RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
  • Roquin-1
KeywordsRNA BINDING PROTEIN / roquin / ROQ domain / RNA binding / CDE2
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 / 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 / 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: 2.4 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Assembly

Deposited unit
A: Roquin-1
E: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
B: Roquin-1
F: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
C: Roquin-1
G: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
D: Roquin-1
H: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,25312
Polymers109,1228
Non-polymers1314
Water5,314295
1
A: Roquin-1
E: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3514
Polymers27,2812
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-27 kcal/mol
Surface area10510 Å2
MethodPISA
2
B: Roquin-1
F: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3163
Polymers27,2812
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-30 kcal/mol
Surface area10560 Å2
MethodPISA
3
C: Roquin-1
G: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')


Theoretical massNumber of molelcules
Total (without water)27,2812
Polymers27,2812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-21 kcal/mol
Surface area10750 Å2
MethodPISA
4
D: Roquin-1
H: RNA (5'-R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3053
Polymers27,2812
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-21 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.530, 160.660, 68.010
Angle α, β, γ (deg.)90.000, 107.960, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
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*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC))-3')


Mass: 6751.968 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 250 mM ammonium sulphate and 30% (v/w) PEG 4000

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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: Sep 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35375 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 55.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01 / Net I/σ(I): 14.05
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 2623 / CC1/2: 0.63 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QI0

4qi0


Resolution: 2.4→42.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 22.289 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.522 / ESU R Free: 0.292
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1720 4.9 %RANDOM
Rwork0.1968 ---
obs0.2001 33655 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164.31 Å2 / Biso mean: 55.195 Å2 / Biso min: 25.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å2-0 Å2-1.1 Å2
2---2.2 Å20 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 2.4→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4803 1796 4 295 6898
Biso mean--56.91 49.2 -
Num. residues----685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126935
X-RAY DIFFRACTIONr_bond_other_d0.0070.0185552
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.5519770
X-RAY DIFFRACTIONr_angle_other_deg1.4151.79512963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66721.237283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25315948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg181548
X-RAY DIFFRACTIONr_chiral_restr0.0930.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026471
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021485
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 116 -
Rwork0.294 2502 -
all-2618 -
obs--99.89 %
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)
11.23260.6248-0.19350.53410.14590.36570.08750.0220.1017-0.00310.027-0.03990.0655-0.0013-0.11450.31330.03660.0830.55530.00310.5005-2.639113.606816.7748
20.7507-0.0055-0.2021.0078-0.04540.70670.1295-0.04180.20150.05850.09740.1019-0.1633-0.2332-0.22680.38510.02510.130.4254-0.04050.5761-14.470925.554325.0498
31.51250.06650.51211.0030.27210.2460.15190.18310.21780.003-0.1576-0.14420.0682-0.02950.00570.26320.07460.16460.60220.09240.5119-14.106618.1173-13.8264
43.3534-0.183-0.12160.0163-0.00510.76660.184-0.05620.57810.02010.0135-0.0794-0.1164-0.5447-0.19760.52970.1099-0.00410.4170.00240.6409-26.000429.0967-3.4347
50.7320.4533-0.03280.9987-0.33710.21360.18080.0717-0.14340.0493-0.09630.1423-0.06010.0555-0.08460.31360.04250.0030.5603-0.02120.5092-36.215-9.1997-7.2441
61.594-0.89220.36011.7731-0.04270.50010.24040.213-0.53150.0632-0.075-0.0609-0.08540.2274-0.16540.37480.0372-0.0690.3447-0.02110.6512-21.6968-21.352-8.5785
70.8152-1.32180.68972.3175-1.16240.5988-0.1025-0.0751-0.31980.06580.41450.5491-0.0789-0.1432-0.3120.3872-0.02780.05130.56980.11910.5586-25.0684-13.213926.409
81.26631.05221.61872.56810.18543.0784-0.110.1722-0.3889-0.11620.289-0.2581-0.15530.2927-0.1790.4343-0.00380.06870.20530.1860.7672-10.5289-25.649127.5099
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A174 - 325
2X-RAY DIFFRACTION2E1 - 21
3X-RAY DIFFRACTION3B177 - 325
4X-RAY DIFFRACTION4F1 - 21
5X-RAY DIFFRACTION5C175 - 325
6X-RAY DIFFRACTION6G1 - 21
7X-RAY DIFFRACTION7D177 - 325
8X-RAY DIFFRACTION8H1 - 21

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