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- PDB-2n5k: Regnase-1 Zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 2n5k
TitleRegnase-1 Zinc finger domain
ComponentsRibonuclease ZC3H12A
KeywordsHYDROLASE / Regnase / Regnase-1 / Zc3h12a / Zinc finger
Function / homology
Function and homology information


immune response-activating signaling pathway / positive regulation of protein deubiquitination / positive regulation of miRNA catabolic process / negative regulation of macrophage activation / miRNA catabolic process / negative regulation of muscle cell apoptotic process / RNA exonuclease activity / rough endoplasmic reticulum membrane / negative regulation of T-helper 17 cell differentiation / cellular response to sodium arsenite ...immune response-activating signaling pathway / positive regulation of protein deubiquitination / positive regulation of miRNA catabolic process / negative regulation of macrophage activation / miRNA catabolic process / negative regulation of muscle cell apoptotic process / RNA exonuclease activity / rough endoplasmic reticulum membrane / negative regulation of T-helper 17 cell differentiation / cellular response to sodium arsenite / host-mediated suppression of viral genome replication / positive regulation of mRNA catabolic process / negative regulation of cardiac muscle contraction / cellular response to ionomycin / 3'-UTR-mediated mRNA destabilization / nuclease activity / positive regulation of lipid storage / negative regulation of nitric oxide biosynthetic process / cellular response to chemokine / mRNA 3'-UTR AU-rich region binding / positive regulation of p38MAPK cascade / negative regulation of non-canonical NF-kappaB signal transduction / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / miRNA binding / negative regulation of interleukin-1 beta production / negative regulation of protein phosphorylation / mRNA catabolic process / negative regulation of type II interferon production / protein complex oligomerization / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / RNA nuclease activity / cellular response to interleukin-1 / positive regulation of execution phase of apoptosis / protein deubiquitination / positive regulation of fat cell differentiation / cellular response to glucose starvation / positive regulation of defense response to virus by host / rough endoplasmic reticulum / RNA endonuclease activity / negative regulation of cytokine production involved in inflammatory response / positive regulation of endothelial cell migration / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / mRNA 3'-UTR binding / P-body / cellular response to virus / positive regulation of protein import into nucleus / RNA stem-loop binding / cellular response to tumor necrosis factor / positive regulation of reactive oxygen species metabolic process / positive regulation of angiogenesis / cytoplasmic ribonucleoprotein granule / nervous system development / T cell receptor signaling pathway / ribosome binding / cellular response to lipopolysaccharide / regulation of gene expression / cellular response to oxidative stress / angiogenesis / cytoskeleton / Hydrolases; Acting on ester bonds / cell differentiation / cysteine-type deubiquitinase activity / inflammatory response / negative regulation of gene expression / mRNA binding / apoptotic process / DNA damage response / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Rege-1, UBA-like domain / Endoribonuclease Regnase 1/ZC3H12, C-terminal domain / UBA-like domain / Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain
Similarity search - Domain/homology
Endoribonuclease ZC3H12A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics
Model detailslowest energy, model1
AuthorsYokogawa, M. / Tsushima, T. / Noda, N.N. / Kumeta, H. / Adachi, W. / Enokizono, Y. / Yamashita, K. / Standley, D.M. / Takeuchi, O. / Akira, S. / Inagaki, F.
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Authors: Yokogawa, M. / Tsushima, T. / Noda, N.N. / Kumeta, H. / Enokizono, Y. / Yamashita, K. / Standley, D.M. / Takeuchi, O. / Akira, S. / Inagaki, F.
History
DepositionJul 18, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5552
Polymers3,4901
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Ribonuclease ZC3H12A


Mass: 3490.069 Da / Num. of mol.: 1 / Fragment: UNP residues 299-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3h12a / Production host: Escherichia coli (E. coli)
References: UniProt: Q5D1E7, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D C(CO)NH
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D (HCA)CO(CA)NH
1913D HNCA
11013D HN(CA)HA
11113D HN(CO)CA
11213D HNCO
11312D (HB)CB(CGCD)HD
11412D (HB)CB(CGCDCE)HE
11513D (H)CCH-TOCSY aliphatic
11613D (H)CCH-TOCSY aromatic
11713D 1H-13C NOESY aliphatic
11813D 1H-15N NOESY
11913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.3 mM [U-99% 13C; U-99% 15N] Reg1_ZnF-1, 10% v/v [U-2H] D2O-2, 5 ug DSS-3, 20 mM HEPES-4, 150 mM sodium chloride-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMReg1_ZnF-1[U-99% 13C; U-99% 15N]1
10 v/vD2O-2[U-2H]1
5 %DSS-31
20 mMHEPES-41
150 mMsodium chloride-51
Sample conditionsIonic strength: 170 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
OliviaMasashi Yokochichemical shift assignment
OliviaMasashi Yokochipeak picking
OliviaMasashi Yokochidata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
rnmrtkv.3JC Hoch and AS Stermprocessing
RefinementMethod: distance geometry, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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