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- PDB-4qil: Crystal structure of the ROQ domain of human Roquin in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4qil
TitleCrystal structure of the ROQ domain of human Roquin in complex with the Hmg19 stem-loop RNA
Components
  • 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP*A)-3'
  • Roquin-1
KeywordsRNA BINDING PROTEIN/RNA / Winged-helix motif / mRNA stem-loop / mRNA decay / immune responses / autoimmunity / RNA BINDING PROTEIN-RNA complex
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
: / 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 ...: / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RNA / RNA (> 10) / Roquin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTan, D. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA.
Authors: Tan, D. / Zhou, M. / Kiledjian, M. / Tong, L.
History
DepositionMay 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Roquin-1
B: Roquin-1
D: 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP*A)-3'
C: 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6506
Polymers86,5704
Non-polymers802
Water1448
1
A: Roquin-1
C: 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3253
Polymers43,2852
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-27 kcal/mol
Surface area17540 Å2
MethodPISA
2
B: Roquin-1
D: 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3253
Polymers43,2852
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-26 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.600, 170.000, 51.100
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211

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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


Mass: 37214.434 Da / Num. of mol.: 2 / Fragment: ROQ domain (UNP residues 88-407)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H1, KIAA2025, RNF198 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5TC82
#2: RNA chain 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP*A)-3'


Mass: 6070.634 Da / Num. of mol.: 2 / Fragment: CDE stem-loop / Source method: obtained synthetically / Details: Hmgxb3 mRNA (Hmg19)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1 M Tris-HCl, pH 8.2, 0.3 M calcium acetate, 12%-14% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 18578 / Num. obs: 17984 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.7 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CBASSdata collection
COMOphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QIK

4qik


Resolution: 2.9→37.696 Å / SU ML: 0.4 / σ(F): 1.38 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 872 4.85 %RANDOM
Rwork0.1948 ---
obs0.1976 17984 96.78 %-
all-18578 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→37.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 678 2 8 5385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015535
X-RAY DIFFRACTIONf_angle_d1.3747640
X-RAY DIFFRACTIONf_dihedral_angle_d15.6662212
X-RAY DIFFRACTIONf_chiral_restr0.055903
X-RAY DIFFRACTIONf_plane_restr0.007874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.08160.3731430.29072572X-RAY DIFFRACTION88
3.0816-3.31940.35991430.24952901X-RAY DIFFRACTION98
3.3194-3.65320.31261720.20642867X-RAY DIFFRACTION99
3.6532-4.18130.23021340.18022941X-RAY DIFFRACTION99
4.1813-5.26570.20961350.17372907X-RAY DIFFRACTION99
5.2657-37.69940.19411450.17072924X-RAY DIFFRACTION98

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