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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 miRNA catabolic process / positive regulation of protein deubiquitination / cellular response to ionomycin / miRNA catabolic process / RNA exonuclease activity / positive regulation of mRNA catabolic process / rough endoplasmic reticulum membrane / negative regulation by host of viral genome replication / cellular response to sodium arsenite ...immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / cellular response to ionomycin / miRNA catabolic process / RNA exonuclease activity / positive regulation of mRNA catabolic process / rough endoplasmic reticulum membrane / negative regulation by host of viral genome replication / cellular response to sodium arsenite / negative regulation of T-helper 17 cell differentiation / negative regulation of muscle cell apoptotic process / nuclease activity / 3'-UTR-mediated mRNA destabilization / positive regulation of lipid storage / negative regulation of cardiac muscle contraction / negative regulation of nitric oxide biosynthetic process / mRNA 3'-UTR AU-rich region binding / cellular response to chemokine / negative regulation of non-canonical NF-kappaB signal transduction / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / miRNA binding / positive regulation of p38MAPK cascade / negative regulation of interleukin-1 beta production / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / positive regulation of execution phase of apoptosis / mRNA catabolic process / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / positive regulation of fat cell differentiation / cellular response to interleukin-1 / cellular response to glucose starvation / positive regulation of autophagy / rough endoplasmic reticulum / negative regulation of canonical NF-kappaB signal transduction / positive regulation of defense response to virus by host / RNA endonuclease activity / positive regulation of endothelial cell migration / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / P-body / cellular response to virus / cytoplasmic ribonucleoprotein granule / positive regulation of protein import into nucleus / RNA stem-loop binding / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / ribosome binding / protein complex oligomerization / cellular response to tumor necrosis factor / nervous system development / T cell receptor signaling pathway / cellular response to oxidative stress / cellular response to lipopolysaccharide / angiogenesis / cysteine-type deubiquitinase activity / Hydrolases; Acting on ester bonds / cell differentiation / cytoskeleton / inflammatory response / negative regulation of gene expression / mRNA binding / apoptotic process / DNA damage response / chromatin binding / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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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