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- PDB-3v32: Crystal structure of MCPIP1 N-terminal conserved domain -

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Basic information

Entry
Database: PDB / ID: 3v32
TitleCrystal structure of MCPIP1 N-terminal conserved domain
ComponentsRibonuclease ZC3H12A
KeywordsHYDROLASE / Rossmann-like sandwich fold / RNase / cytoplastic
Function / homology
Function and homology information


immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / negative regulation of macrophage activation / negative regulation of muscle cell apoptotic process / RNA exonuclease activity / miRNA catabolic process / Regulation of CDH19 Expression and Function / negative regulation of T-helper 17 cell differentiation / rough endoplasmic reticulum membrane ...immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / negative regulation of macrophage activation / negative regulation of muscle cell apoptotic process / RNA exonuclease activity / miRNA catabolic process / Regulation of CDH19 Expression and Function / negative regulation of T-helper 17 cell differentiation / rough endoplasmic reticulum membrane / positive regulation of mRNA catabolic process / host-mediated suppression of viral genome replication / cellular response to sodium arsenite / negative regulation of cardiac muscle contraction / cellular response to ionomycin / 3'-UTR-mediated mRNA destabilization / negative regulation of nitric oxide biosynthetic process / positive regulation of lipid storage / 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 / miRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of interleukin-1 beta production / negative regulation of protein phosphorylation / protein complex oligomerization / negative regulation of interleukin-6 production / negative regulation of type II interferon production / positive regulation of execution phase of apoptosis / negative regulation of tumor necrosis factor production / cellular response to interleukin-1 / protein deubiquitination / positive regulation of fat cell differentiation / RNA nuclease activity / cellular response to glucose starvation / positive regulation of defense response to virus by host / negative regulation of canonical NF-kappaB signal transduction / positive regulation of autophagy / negative regulation of cytokine production involved in inflammatory response / RNA endonuclease activity / positive regulation of endothelial cell migration / mRNA 3'-UTR binding / P-body / cellular response to virus / positive regulation of protein import into nucleus / RNA stem-loop binding / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / cellular response to tumor necrosis factor / nervous system development / T cell receptor signaling pathway / regulation of gene expression / ribosome binding / cellular response to lipopolysaccharide / cellular response to oxidative stress / angiogenesis / defense response to virus / Hydrolases; Acting on ester bonds / cell differentiation / cytoskeleton / inflammatory response / 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 / Rossmann fold - #11980 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease ZC3H12A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsXu, J. / Peng, W. / Sun, Y. / Wang, X. / Xu, Y. / Li, X. / Gao, G. / Rao, Z.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural study of MCPIP1 N-terminal conserved domain reveals a PIN-like RNase
Authors: Xu, J. / Peng, W. / Sun, Y. / Wang, X. / Xu, Y. / Li, X. / Gao, G. / Rao, Z.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ribonuclease ZC3H12A
A: Ribonuclease ZC3H12A


Theoretical massNumber of molelcules
Total (without water)42,5792
Polymers42,5792
Non-polymers00
Water2,990166
1
B: Ribonuclease ZC3H12A


Theoretical massNumber of molelcules
Total (without water)21,2891
Polymers21,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ribonuclease ZC3H12A


Theoretical massNumber of molelcules
Total (without water)21,2891
Polymers21,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.350, 56.350, 113.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Ribonuclease ZC3H12A / MCPIP1 / MCP-induced protein 1 / Zinc finger CCCH domain-containing protein 12A


Mass: 21289.305 Da / Num. of mol.: 2 / Fragment: N-terminal conserved domain, residues 112-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCPIP1 / Plasmid: pGEX 6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5D1E8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 7% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2009
RadiationMonochromator: flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.94 Å / Num. all: 23856 / Num. obs: 21614 / % possible obs: 90.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2 / Num. unique all: 1219 / % possible all: 51.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.94 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8214 / σ(F): 1.38 / Phase error: 25.59 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1161 5.38 %RANDOM
Rwork0.2016 ---
all0.21 23835 --
obs0.2059 21578 90.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.21 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 60.69 Å2 / Biso mean: 24.1556 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1-3.3607 Å20 Å2-0 Å2
2--3.3607 Å20 Å2
3----6.7214 Å2
Refinement stepCycle: LAST / Resolution: 2→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 0 166 2754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082628
X-RAY DIFFRACTIONf_angle_d1.0753552
X-RAY DIFFRACTIONf_chiral_restr0.075378
X-RAY DIFFRACTIONf_plane_restr0.004464
X-RAY DIFFRACTIONf_dihedral_angle_d17.6641002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.09120.2864830.22421494157750
2.0912-2.20120.24071290.21212150227973
2.2012-2.33880.26921420.22412666280890
2.3388-2.51890.28571370.21642797293495
2.5189-2.77140.25981470.22192818296595
2.7714-3.17010.2731670.21122817298494
3.1701-3.98550.24431390.19792850298995
3.9855-16.99810.20041570.17992845300295

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