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- PDB-5h9w: Crystal structure of Regnase PIN domain, form II -

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Basic information

Entry
Database: PDB / ID: 5h9w
TitleCrystal structure of Regnase PIN domain, form II
ComponentsRibonuclease ZC3H12A
KeywordsHYDROLASE / RNase
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 / negative regulation of interleukin-1 beta production / positive regulation of p38MAPK cascade / 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 / negative regulation of canonical NF-kappaB signal transduction / rough endoplasmic reticulum / 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 / Rossmann fold - #11980 / Ribonuclease Zc3h12a-like, NYN domain / Zc3h12a-like Ribonuclease NYN domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease ZC3H12A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYokogawa, M. / Tsushima, T. / Adachi, W. / Noda, N.N. / Inagaki, F.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS Japan
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
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease ZC3H12A
B: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1074
Polymers49,0612
Non-polymers462
Water61334
1
A: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5532
Polymers24,5301
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5532
Polymers24,5301
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.333, 113.333, 78.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 134 - 295 / Label seq-ID: 5 - 166

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ribonuclease ZC3H12A / Regnase-1 / MCP-induced protein 1 / Zinc finger CCCH domain-containing protein 12A


Mass: 24530.289 Da / Num. of mol.: 2 / Fragment: PIN domain, UNP residues 134-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3h12a, Mcpip, Mcpip1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5D1E7, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.7 M NaCl, 100 mM HEPES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→26.94 Å / Num. obs: 16940 / % possible obs: 92.9 % / Redundancy: 10.4 % / Net I/σ(I): 34.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 7.9 / % possible all: 67.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H9V

5h9v


Resolution: 2.6→26.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.815 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23142 862 5.1 %RANDOM
Rwork0.19144 ---
obs0.19347 16057 92.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.875 Å2
Baniso -1Baniso -2Baniso -3
1--3.21 Å2-3.21 Å2-0 Å2
2---3.21 Å2-0 Å2
3---10.41 Å2
Refinement stepCycle: 1 / Resolution: 2.6→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 2 34 2694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192722
X-RAY DIFFRACTIONr_bond_other_d0.0050.022632
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9583677
X-RAY DIFFRACTIONr_angle_other_deg1.15536045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65122.662139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72215485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4951531
X-RAY DIFFRACTIONr_chiral_restr0.090.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213037
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1164.0121294
X-RAY DIFFRACTIONr_mcbond_other3.1154.0121293
X-RAY DIFFRACTIONr_mcangle_it4.6886.0171614
X-RAY DIFFRACTIONr_mcangle_other4.6876.0171615
X-RAY DIFFRACTIONr_scbond_it3.6764.3981428
X-RAY DIFFRACTIONr_scbond_other3.6754.3981429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6176.4492064
X-RAY DIFFRACTIONr_long_range_B_refined7.40231.8273089
X-RAY DIFFRACTIONr_long_range_B_other7.40131.8253084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9669 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 46 -
Rwork0.302 833 -
obs--65.84 %
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)
15.887-0.29630.64983.13370.59182.88970.2362-0.2788-0.1322-0.028-0.0891-0.16770.17470.1682-0.14710.0818-0.0312-0.09790.312-0.05620.2191-12.213346.4856-10.8473
24.30850.8950.40951.81930.44093.12830.12950.9185-0.0683-0.2696-0.08530.0029-0.0368-0.0603-0.04420.11670.1797-0.02280.4241-0.03140.23516.078647.9781-15.9622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 295
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1A501 - 515
4X-RAY DIFFRACTION1B509 - 518
5X-RAY DIFFRACTION2B134 - 295
6X-RAY DIFFRACTION2B401

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