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- PDB-3v33: Crystal structure of MCPIP1 conserved domain with zinc-finger motif -

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Basic information

Entry
Database: PDB / ID: 3v33
TitleCrystal structure of MCPIP1 conserved domain with zinc-finger motif
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 / cellular response to ionomycin / miRNA catabolic process / Regulation of CDH19 Expression and Function / negative regulation of macrophage activation / RNA exonuclease activity / positive regulation of mRNA catabolic process / rough endoplasmic reticulum membrane ...immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / cellular response to ionomycin / miRNA catabolic process / Regulation of CDH19 Expression and Function / negative regulation of macrophage activation / 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 / 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 / miRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of interleukin-1 beta production / positive regulation of p38MAPK cascade / positive regulation of execution phase of apoptosis / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / 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 / RNA nuclease activity / cellular response to glucose starvation / positive regulation of autophagy / RNA stem-loop binding / negative regulation of canonical NF-kappaB signal transduction / RNA endonuclease activity / positive regulation of defense response to virus by host / positive regulation of endothelial cell migration / negative regulation of protein phosphorylation / mRNA 3'-UTR binding / P-body / cellular response to virus / positive regulation of protein import into nucleus / cytoplasmic ribonucleoprotein granule / 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 / cellular response to oxidative stress / T cell receptor signaling pathway / regulation of gene expression / angiogenesis / defense response to virus / cellular response to lipopolysaccharide / 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 / RNA binding / nucleoplasm / metal ion binding / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 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
A: Ribonuclease ZC3H12A
B: Ribonuclease ZC3H12A


Theoretical massNumber of molelcules
Total (without water)51,5452
Polymers51,5452
Non-polymers00
Water2,144119
1
A: Ribonuclease ZC3H12A


Theoretical massNumber of molelcules
Total (without water)25,7731
Polymers25,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease ZC3H12A


Theoretical massNumber of molelcules
Total (without water)25,7731
Polymers25,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.531, 113.531, 78.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

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Components

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


Mass: 25772.594 Da / Num. of mol.: 2
Fragment: N-terminal conserved domain with the zinc-finger motif, residues 112-334
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 / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4% Tacsimate, 6% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 13, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→36.26 Å / Num. all: 39295 / Num. obs: 30650 / % possible obs: 78 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 32.81 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.35 / % possible all: 33.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.005→36.259 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7982 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1432 4.89 %RANDOM
Rwork0.19 27873 --
obs0.1918 29305 74.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.605 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 141.18 Å2 / Biso mean: 47.5958 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--3.2501 Å2-0 Å20 Å2
2---3.2501 Å20 Å2
3---6.5002 Å2
Refinement stepCycle: LAST / Resolution: 2.005→36.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 0 119 2779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082724
X-RAY DIFFRACTIONf_angle_d1.0833678
X-RAY DIFFRACTIONf_chiral_restr0.078391
X-RAY DIFFRACTIONf_plane_restr0.005479
X-RAY DIFFRACTIONf_dihedral_angle_d12.521050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0046-2.07630.2872320.243464868018
2.0763-2.15940.2716660.23231434150039
2.1594-2.25770.264940.2312002209654
2.2577-2.37670.26221130.24042482259567
2.3767-2.52550.27921520.23662879303177
2.5255-2.72050.30412030.24063483368695
2.7205-2.99410.25321920.22737333925100
2.9941-3.42710.23441760.198937373913100
3.4271-4.31670.1881950.15513741393699
4.3167-36.26450.19982090.16193734394397
Refinement TLS params.Method: refined / Origin x: -58.4348 Å / Origin y: 0.746 Å / Origin z: 10.4629 Å
111213212223313233
T0.398 Å20.2627 Å2-0.0225 Å2--0.006 Å20.0241 Å2--0.1351 Å2
L0.0315 °2-0.0129 °20.014 °2-0.0584 °2-0.0299 °2--0.0256 °2
S0.0814 Å °0.0925 Å °0.0312 Å °-0.1431 Å °-0.0422 Å °0.0203 Å °0.0089 Å °-0.0315 Å °0.0178 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA134 - 296
2X-RAY DIFFRACTION1allB134 - 296
3X-RAY DIFFRACTION1allA401 - 469
4X-RAY DIFFRACTION1allB401 - 450

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