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- PDB-3v34: Crystal structure of MCPIP1 conserved domain with magnesium ion i... -

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Basic information

Entry
Database: PDB / ID: 3v34
TitleCrystal structure of MCPIP1 conserved domain with magnesium ion in the catalytic center
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 / Regulation of CDH19 Expression and Function / miRNA catabolic process / 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 / Regulation of CDH19 Expression and Function / miRNA catabolic process / 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 / 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 / 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 / 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 / regulation of gene expression / cellular response to lipopolysaccharide / angiogenesis / defense response to virus / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,6274
Polymers42,5792
Non-polymers492
Water2,828157
1
A: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3142
Polymers21,2891
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3142
Polymers21,2891
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.349, 56.349, 113.574
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M 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 315 / Detector: CCD / Date: Mar 16, 2011
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→25.36 Å / Num. all: 23807 / Num. obs: 23308 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2184 / % possible all: 92.2

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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: 2.003→25.356 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8315 / SU ML: 0.29 / σ(F): 0 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1111 5.11 %RANDOM
Rwork0.198 ---
obs0.2001 21748 91.35 %-
all-23807 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.596 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 78.81 Å2 / Biso mean: 28.2229 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1-6.2605 Å20 Å2-0 Å2
2--6.2605 Å20 Å2
3----12.521 Å2
Refinement stepCycle: LAST / Resolution: 2.003→25.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 2 157 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082660
X-RAY DIFFRACTIONf_angle_d1.0663596
X-RAY DIFFRACTIONf_chiral_restr0.074385
X-RAY DIFFRACTIONf_plane_restr0.006469
X-RAY DIFFRACTIONf_dihedral_angle_d14.0811022
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 (%)
2.0025-2.09360.32531260.24992186231278
2.0936-2.20390.23051300.22082478260889
2.2039-2.34190.27341270.20082514264189
2.3419-2.52260.23041460.21032577272392
2.5226-2.77620.26741450.20062597274292
2.7762-3.17730.22531380.2052730286896
3.1773-4.00050.25311440.18682781292598
4.0005-25.35840.20831550.18342774292997

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