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- PDB-8rhs: Structure of the ZnF domain from human Roquin-1 -

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Basic information

Entry
Database: PDB / ID: 8rhs
TitleStructure of the ZnF domain from human Roquin-1
ComponentsRoquin-1
KeywordsRNA BINDING PROTEIN / ZnF / Roquin / C3H1 / Immune-regulation
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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSchlundt, A. / Tants, J.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHL2062/2-1 Germany
German Research Foundation (DFG)SCHL2062/2-2 Germany
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger.
Authors: Tants, J.N. / Oberstrass, L. / Weigand, J.E. / Schlundt, A.
History
DepositionDec 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Roquin-1


Theoretical massNumber of molelcules
Total (without water)5,5821
Polymers5,5821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide 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: 5581.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C3H1-type of zinc finger / Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H1, KIAA2025, RNF198 / Plasmid: pETTrx1a / Details (production host): His6-Trx-TEV
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: Q5TC82, RING-type E3 ubiquitin transferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic31D
121isotropic12D 1H-15N HSQC
132isotropic32D 1H-13C HSQC aliphatic
142isotropic32D 1H-13C HSQC aromatic
151isotropic23D 1H-15N NOESY
192isotropic33D 1H-13C NOESY aromatic
182isotropic33D 1H-13C NOESY aliphatic
172isotropic13D HN(CA)CB
162isotropic13D HBHANH
1112isotropic13D HN(CA)CO
1102isotropic13D HNCO
1122isotropic33D CCH TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.36 mM [U-15N] Human Roquin-1 zinc finger domain, 25 mM TRIS, 150 mM sodium chloride, 2 mM TCEP, 0.02 mg/mL Zinc, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.74 mM [U-100% 13C; U-100% 15N] Human Roquin-1 zinc finger domain, 25 mM TRIS, 150 mM sodium chloride, 2 mM TCEP, 0.02 mM Zinc, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.36 mMHuman Roquin-1 zinc finger domain[U-15N]1
25 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
2 mMTCEPnatural abundance1
0.02 mg/mLZincnatural abundance1
0.74 mMHuman Roquin-1 zinc finger domain[U-100% 13C; U-100% 15N]2
25 mMTRISnatural abundance2
150 mMsodium chloridenatural abundance2
2 mMTCEPnatural abundance2
0.02 mMZincnatural abundance2
Sample conditionsIonic strength: 0.15 M / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.xBruker Biospincollection
TopSpin3.xBruker Biospinprocessing
CcpNmr Analysis2.1CCPNchemical shift assignment
CcpNmr Analysis2.1CCPNpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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