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- PDB-7ndh: Crystal structure of ZC3H12C PIN domain -

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Basic information

Entry
Database: PDB / ID: 7ndh
TitleCrystal structure of ZC3H12C PIN domain
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 / hydrolase activity / mRNA binding / zinc ion binding / nucleus
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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable ribonuclease ZC3H12C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,93311
Polymers39,4132
Non-polymers5209
Water4,684260
1
A: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9555
Polymers19,7071
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9786
Polymers19,7071
Non-polymers2715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.331, 80.331, 143.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPVALVALchain AAA260 - 4281 - 169
2GLYGLYPROPROchain BBB262 - 4263 - 167

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Components

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


Mass: 19706.611 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 20% PEG 6000 and 0.1 M HEPES pH 7.0

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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: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.94→44.5 Å / Num. obs: 35462 / % possible obs: 99.88 % / Redundancy: 7.53 % / CC1/2: 0.999 / Net I/σ(I): 20.5
Reflection shellResolution: 1.94→2.06 Å / Num. unique obs: 3484 / CC1/2: 0.692 / % possible all: 99.8

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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: 1.94→44.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 1774 5 %
Rwork0.1723 33688 -
obs0.1744 35462 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.35 Å2 / Biso mean: 42.8204 Å2 / Biso min: 19.24 Å2
Refinement stepCycle: final / Resolution: 1.94→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 33 260 3005
Biso mean--45.63 48.99 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152803
X-RAY DIFFRACTIONf_angle_d1.3993769
X-RAY DIFFRACTIONf_chiral_restr0.074401
X-RAY DIFFRACTIONf_plane_restr0.008493
X-RAY DIFFRACTIONf_dihedral_angle_d11.7771073
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1568X-RAY DIFFRACTION7.207TORSIONAL
12B1568X-RAY DIFFRACTION7.207TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.94-1.99220.29321340.2626253499
1.9922-2.05080.24431340.2352551100
2.0508-2.1170.27891330.21442522100
2.117-2.19260.24161340.19062554100
2.1926-2.28040.2081350.18582556100
2.2804-2.38420.24061340.18042549100
2.3842-2.50990.24151350.17832575100
2.5099-2.66710.20631350.19022570100
2.6671-2.8730.2371370.18552594100
2.873-3.16210.22881370.18262604100
3.1621-3.61950.20721370.17262603100
3.6195-4.55940.19591400.1382669100
4.5594-44.50.18021490.15632807100
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)
15.2846-4.5163-0.69928.1715-3.80514.6566-0.04690.0132-0.11050.00120.07960.1865-0.1415-0.1171-0.0740.2416-0.10640.00670.1346-0.04010.1875-4.37135.34033.5126
23.12320.16730.11255.2768-4.96017.3868-0.0471-0.18460.13970.46460.0951-0.0366-0.66910.0773-0.03020.2639-0.0583-0.00140.1573-0.06290.1591-3.604439.25617.234
38.29561.93675.33677.47162.58924.2344-0.18570.46790.9981-0.432-0.10480.1447-0.93630.04740.34010.27270.00210.03940.26460.02260.3313-8.021349.1766-1.0945
43.8861.9321-2.84875.2567-3.94336.37480.10460.20430.2039-0.23960.25820.1519-0.08990.2549-0.38550.2524-0.0956-0.04380.2246-0.01190.26573.474446.7329-7.0565
57.0987-5.25084.61464.7417-5.72399.56320.21770.5928-0.0534-0.6125-0.3015-0.68160.25170.7090.12470.2834-0.06960.04690.339-0.03850.36358.955934.1216-1.2893
68.0972-1.2879-1.64275.3390.92613.3651-0.04690.4409-0.3974-0.30390.1089-0.42080.20040.0603-0.02970.2679-0.07790.00820.1796-0.02420.25180.756127.0884-0.0063
75.04081.778-2.91977.136-0.84453.66570.3705-0.7041-0.94020.4849-0.1933-0.34560.81990.0876-0.19830.4292-0.0339-0.08440.30760.09670.4365-0.206219.798612.4236
85.11012.7053-1.34515.649-0.677.64770.0791-0.1646-0.29140.4111-0.3625-0.2994-0.0595-0.05650.26530.2729-0.1613-0.04240.29180.0120.321917.384353.29720.109
93.22711.4209-0.10817.11471.26123.02910.3745-0.3158-0.43760.6014-0.2899-1.08940.11840.2876-0.08890.2894-0.1504-0.0920.36530.06670.450423.005252.83891.8619
107.25521.1847-0.97973.8462-1.69223.27120.875-1.38440.60421.4079-0.631-0.3337-0.88580.2889-0.38650.786-0.4369-0.00330.6764-0.01430.449719.930361.565312.0269
119.4833-3.1985-0.39376.40460.49594.33820.591-0.32380.47330.494-0.41150.2879-0.2258-0.5769-0.17980.3192-0.20260.07720.4326-0.01890.426719.916370.54162.4545
123.22320.33421.69574.55144.39624.8754-0.25880.43060.256-0.2125-0.2652-0.0454-0.5276-0.12650.45440.3635-0.14460.01250.36560.03560.318820.512162.6724-10.3745
134.69461.41810.9384.0026-0.71013.2413-0.1810.29260.1937-0.33930.132-0.1179-0.19420.07370.06990.298-0.14650.02760.2944-0.04210.263914.09154.0024-9.5388
143.703-1.10913.41635.3826-1.84196.43240.07560.4152-0.8178-0.89280.2355-0.80160.49940.0838-0.1990.4119-0.10610.1260.3435-0.15950.433417.002641.5878-13.4781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 261 through 286 )A261 - 286
2X-RAY DIFFRACTION2chain 'A' and (resid 287 through 314 )A287 - 314
3X-RAY DIFFRACTION3chain 'A' and (resid 315 through 334 )A315 - 334
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 354 )A335 - 354
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 365 )A355 - 365
6X-RAY DIFFRACTION6chain 'A' and (resid 366 through 406 )A366 - 406
7X-RAY DIFFRACTION7chain 'A' and (resid 407 through 428 )A407 - 428
8X-RAY DIFFRACTION8chain 'B' and (resid 262 through 286 )B262 - 286
9X-RAY DIFFRACTION9chain 'B' and (resid 287 through 314 )B287 - 314
10X-RAY DIFFRACTION10chain 'B' and (resid 315 through 334 )B315 - 334
11X-RAY DIFFRACTION11chain 'B' and (resid 335 through 354 )B335 - 354
12X-RAY DIFFRACTION12chain 'B' and (resid 355 through 365 )B355 - 365
13X-RAY DIFFRACTION13chain 'B' and (resid 366 through 406 )B366 - 406
14X-RAY DIFFRACTION14chain 'B' and (resid 407 through 425 )B407 - 425

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