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- PDB-7ndi: Crystal structure of ZC3H12C PIN domain with Mg2+ Ion -

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Basic information

Entry
Database: PDB / ID: 7ndi
TitleCrystal structure of ZC3H12C PIN domain with Mg2+ Ion
ComponentsProbable ribonuclease ZC3H12C
KeywordsRNA BINDING PROTEIN / Endo-ribonuclease / Regnase
Function / homology
Function and homology information


RNA endonuclease activity / cytoplasmic ribonucleoprotein granule / Hydrolases; Acting on ester bonds / mRNA binding / nucleus / metal ion binding
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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
Probable ribonuclease ZC3H12C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.875 Å
AuthorsGarg, A. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases.
Authors: Garg, A. / Roske, Y. / Yamada, S. / Uehata, T. / Takeuchi, O. / Heinemann, U.
History
DepositionFeb 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Probable ribonuclease ZC3H12C
B: Probable ribonuclease ZC3H12C
C: Probable ribonuclease ZC3H12C
D: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,48114
Polymers77,1284
Non-polymers35210
Water3,693205
1
A: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4545
Polymers19,2821
Non-polymers1714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3062
Polymers19,2821
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3914
Polymers19,2821
Non-polymers1093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3293
Polymers19,2821
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.701, 114.701, 257.309
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPchain AAA131 - 2951 - 165
2ASPASPchain BBB131 - 2951 - 165
3ASPASPchain CCC131 - 2951 - 165
4GLYGLYchain DDD132 - 2952 - 165

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Components

#1: Protein
Probable ribonuclease ZC3H12C / Zinc finger CCCH domain-containing protein 12C


Mass: 19282.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3h12c, Kiaa1726 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5DTV4, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 6.34 Å3/Da / Density % sol: 80.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 50 mM MgSO4 and 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.87→48.77 Å / Num. obs: 45274 / % possible obs: 99.53 % / Redundancy: 5.77 % / CC1/2: 0.997 / Net I/σ(I): 13.44
Reflection shellResolution: 2.875→2.978 Å / Num. unique obs: 4314 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v34

3v34


Resolution: 2.875→48.767 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 2096 4.63 %
Rwork0.1918 43149 -
obs0.1928 45245 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.65 Å2 / Biso mean: 59.82 Å2 / Biso min: 44.61 Å2
Refinement stepCycle: final / Resolution: 2.875→48.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 19 205 5594
Biso mean--74.36 63.16 -
Num. residues----659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025499
X-RAY DIFFRACTIONf_angle_d0.6827411
X-RAY DIFFRACTIONf_chiral_restr0.03787
X-RAY DIFFRACTIONf_plane_restr0.003972
X-RAY DIFFRACTIONf_dihedral_angle_d10.22108
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3226X-RAY DIFFRACTION8.22TORSIONAL
12B3226X-RAY DIFFRACTION8.22TORSIONAL
13C3226X-RAY DIFFRACTION8.22TORSIONAL
14D3226X-RAY DIFFRACTION8.22TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8752-2.9420.36871330.3278273096
2.942-3.01560.32261380.31632843100
3.0156-3.09710.35091370.28022841100
3.0971-3.18820.30291380.26092832100
3.1882-3.29110.28711370.24252832100
3.2911-3.40870.30821380.25862841100
3.4087-3.54520.25041390.24222863100
3.5452-3.70650.25571400.20862885100
3.7065-3.90180.24931390.19892856100
3.9018-4.14610.16761400.17642888100
4.1461-4.46610.16921400.14912874100
4.4661-4.91510.14121410.13392904100
4.9151-5.62540.18031420.14622916100
5.6254-7.0840.17561440.16992957100
7.084-48.7670.17811500.1655308799
Refinement TLS params.Method: refined / Origin x: 107.1049 Å / Origin y: 85.0175 Å / Origin z: 21.2785 Å
111213212223313233
T0.6382 Å2-0.0413 Å20.0405 Å2-0.2215 Å2-0.003 Å2--0.8617 Å2
L0.4993 °20.0841 °20.2541 °2-0.7148 °20.3699 °2--0.7879 °2
S-0.3044 Å °-0.0664 Å °-0.0635 Å °0.0594 Å °0.29 Å °0.0187 Å °0.0528 Å °-0.111 Å °-0.0221 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA131 - 295
2X-RAY DIFFRACTION1allB131 - 295
3X-RAY DIFFRACTION1allC131 - 295
4X-RAY DIFFRACTION1allD132 - 295
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allG5 - 258
7X-RAY DIFFRACTION1allH1 - 3
8X-RAY DIFFRACTION1allI1 - 2
9X-RAY DIFFRACTION1allI3

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