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- PDB-7ndj: Crystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA h... -

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Basic information

Entry
Database: PDB / ID: 7ndj
TitleCrystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA heptamer
Components
  • Probable ribonuclease ZC3H12C
  • RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')
KeywordsRNA BINDING PROTEIN / Endo-ribonuclease / Regnase
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / zinc 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 / 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
RNA / Probable ribonuclease ZC3H12C
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 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 1.1May 26, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Jun 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 1.3Jan 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
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: Probable ribonuclease ZC3H12C
B: Probable ribonuclease ZC3H12C
C: RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,72814
Polymers47,1203
Non-polymers60811
Water6,774376
1
A: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6975
Polymers22,4881
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribonuclease ZC3H12C
C: RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0319
Polymers24,6322
Non-polymers3997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.248, 63.248, 114.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein / RNA chain , 2 types, 3 molecules ABC

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


Mass: 22488.010 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: RNA chain RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')


Mass: 2144.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 387 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350 and 0.2 M NaF pH 6.9

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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: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.649→44.723 Å / Num. obs: 53908 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.998 / Net I/σ(I): 11.04
Reflection shellResolution: 1.649→1.75 Å / Num. unique obs: 8680 / CC1/2: 0.758

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NDI

7ndi


Resolution: 1.649→44.723 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 2097 3.9 %
Rwork0.175 51736 -
obs0.1763 53833 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.66 Å2 / Biso mean: 36.1081 Å2 / Biso min: 15.21 Å2
Refinement stepCycle: final / Resolution: 1.649→44.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 121 35 376 3423
Biso mean--37.53 43.94 -
Num. residues----364
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.649-1.68720.32231380.3312339198
1.6872-1.72930.35821390.291343699
1.7293-1.77610.30431390.27413424100
1.7761-1.82840.27111390.2424344799
1.8284-1.88740.27471400.2316343199
1.8874-1.95480.25151390.2219344999
1.9548-2.03310.25811400.21083450100
2.0331-2.12560.21851400.18583458100
2.1256-2.23770.19861400.17463451100
2.2377-2.37790.22531400.17163447100
2.3779-2.56150.21181410.17163474100
2.5615-2.81920.19281390.1739342399
2.8192-3.22710.19061400.16933472100
3.2271-4.06530.21111420.14543486100
4.0653-44.7230.1531410.1426349799
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)
13.1399-0.48570.42072.277-0.11824.32690.05110.08540.2387-0.0439-0.08770.0325-0.7204-0.1910.03340.28470.0197-0.00350.13250.00470.168463.27495.2984124.9211
24.288-0.43373.37660.8777-0.56213.55220.0898-0.1584-0.24720.03740.05790.12970.0466-0.0905-0.13520.19820.02530.03550.18540.00630.171560.0149-4.6428115.791
31.3479-0.5533-0.05782.95420.873.5976-0.0165-0.0222-0.09490.07210.0095-0.1520.04290.327-0.00360.15410.0078-0.01170.19960.02860.190171.9778-7.5211132.35
42.686-0.0320.32994.1850.17734.50360.21420.0201-0.24670.0023-0.0716-0.05610.76310.319-0.05990.25220.0584-0.02270.14210.0030.187399.5045-34.0494118.8056
51.1229-0.9434-0.04072.416-0.89014.08780.0996-0.0847-0.08130.07040.07190.34250.4665-0.4988-0.19260.2089-0.05090.01660.1960.00660.206689.9808-29.6718124.9981
65.03482.0518-1.8855.33542.21655.20440.2277-0.13370.291-0.1049-0.26750.4967-0.3617-0.58490.02530.20080.10120.02310.26520.03020.28683.3969-18.0922118.0763
72.17750.85550.88357.80460.8182.48430.21730.24380.3907-0.2335-0.2058-0.0461-0.34570.14750.03430.25760.03940.0820.2050.04470.220999.0766-18.2752108.6034
84.903-2.5486-0.62264.00651.00911.90960.1258-0.4757-0.72010.1091-0.4719-0.20621.95191.09810.23470.85030.23870.03370.48570.14040.4551103.040512.5738105.1933
92.1209-0.5364-0.24860.14390.06470.0357-0.2059-0.32051.23210.0730.33520.4308-1.1333-0.6897-0.04410.72380.1547-0.01450.434-0.02430.6945113.445813.7292106.8168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 204 )A132 - 204
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 236 )A205 - 236
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 297 )A237 - 297
4X-RAY DIFFRACTION4chain 'B' and (resid 132 through 204 )B132 - 204
5X-RAY DIFFRACTION5chain 'B' and (resid 205 through 246 )B205 - 246
6X-RAY DIFFRACTION6chain 'B' and (resid 247 through 263 )B247 - 263
7X-RAY DIFFRACTION7chain 'B' and (resid 264 through 300 )B264 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 301 through 323 )B301 - 323
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 7 )C1 - 7

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