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- PDB-6sjd: ZC3H12B-ribonuclease domain bound to RNA -

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Basic information

Entry
Database: PDB / ID: 6sjd
TitleZC3H12B-ribonuclease domain bound to RNA
Components
  • Probable ribonuclease ZC3H12B
  • RNA (5'-R(*UP*GP*CP*GP*AP*CP*AP*GP*UP*CP*GP*GP*UP*AP*GP*CP*A)-3')
KeywordsRNA BINDING PROTEIN / PIN RNase domain / splice donor sequence RNA / degradation of cytoplasmic viral and/or unspliced transcripts
Function / homology
Function and homology information


: / RNA endonuclease activity / cytoplasmic ribonucleoprotein granule / Hydrolases; Acting on ester bonds / mRNA binding / metal 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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
CACODYLATE ION / RNA / RNA (> 10) / Probable ribonuclease ZC3H12B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.29 Å
AuthorsMorgunova, E. / Bourenkov, G. / Taipale, J.
CitationJournal: Genome Res. / Year: 2020
Title: Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences.
Authors: Jolma, A. / Zhang, J. / Mondragon, E. / Morgunova, E. / Kivioja, T. / Laverty, K.U. / Yin, Y. / Zhu, F. / Bourenkov, G. / Morris, Q. / Hughes, T.R. / Maher 3rd, L.J. / Taipale, J.
History
DepositionAug 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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
Revision 1.2Aug 19, 2020Group: 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 24, 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
B: Probable ribonuclease ZC3H12B
A: Probable ribonuclease ZC3H12B
D: RNA (5'-R(*UP*GP*CP*GP*AP*CP*AP*GP*UP*CP*GP*GP*UP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5596
Polymers48,3743
Non-polymers1863
Water45025
1
B: Probable ribonuclease ZC3H12B
A: Probable ribonuclease ZC3H12B
D: RNA (5'-R(*UP*GP*CP*GP*AP*CP*AP*GP*UP*CP*GP*GP*UP*AP*GP*CP*A)-3')
hetero molecules

B: Probable ribonuclease ZC3H12B
A: Probable ribonuclease ZC3H12B
D: RNA (5'-R(*UP*GP*CP*GP*AP*CP*AP*GP*UP*CP*GP*GP*UP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,11912
Polymers96,7476
Non-polymers3716
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)114.237, 114.237, 165.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21(chain A and (resid 1 or resid 185 through 352))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain BB185 - 1001
211(chain A and (resid 1 or resid 185 through 352))A0

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Components

#1: Protein Probable ribonuclease ZC3H12B / MCP-induced protein 2 / Zinc finger CCCH domain-containing protein 12B


Mass: 20810.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZC3H12B, CXorf32, MCPIP2 / Plasmid: PETG20A-SBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q5HYM0, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(*UP*GP*CP*GP*AP*CP*AP*GP*UP*CP*GP*GP*UP*AP*GP*CP*A)-3')


Mass: 6752.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 5.87 Å3/Da / Density % sol: 79.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: magnesium chloride, sodium cacodilate, 2-methyl-2,4-pentandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.29→93.972 Å / Num. obs: 13344 / % possible obs: 94.3 % / Redundancy: 25.5 % / Biso Wilson estimate: 106.62 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.436 / Rpim(I) all: 0.088 / Rrim(I) all: 0.445 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.291-3.53226.75.3576680.271.0515.46158.1
10.198-93.972519.90.0726660.9970.0170.07599.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.9 Å93.97 Å
Translation3.9 Å93.97 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V33

3v33


Resolution: 3.29→66.954 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 684 5.13 %
Rwork0.2349 12653 -
obs0.2371 13337 77.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 439.75 Å2 / Biso mean: 134.8022 Å2 / Biso min: 24.66 Å2
Refinement stepCycle: final / Resolution: 3.29→66.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 363 7 25 3242
Biso mean--184.29 74.98 -
Num. residues----363
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1516X-RAY DIFFRACTION20.314TORSIONAL
12A1516X-RAY DIFFRACTION20.314TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2902-3.54430.412350.348969722
3.5443-3.90090.3471070.303212166
3.9009-4.46530.2861660.2324313697
4.4653-5.62530.21841820.21213257100
5.6253-66.9540.29591940.23093442100
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)
10.051-0.0296-0.04320.27380.03180.06540.0198-0.1026-0.21190.28780.11310.16210.0652-0.03980.19430.8980.0058-0.2563-0.0463-0.08510.350928.9235-16.2014-17.4003
20.03190.0857-0.00670.1873-0.00040.01440.04-0.0137-0.14190.11480.0159-0.30450.1567-0.02060.20121.0353-0.0094-0.1659-0.19270.11060.356723.8196-43.7198-20.0682
30.0085-0.01860.00830.03450.01060.0040.21650.07680.07790.04440.03940.0953-0.1841-0.09990.00010.65860.01570.03530.6412-0.10981.221412.5841-10.5366-41.6086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 185 through 352)B185 - 352
2X-RAY DIFFRACTION2(chain 'A' and resid 184 through 361)A184 - 361
3X-RAY DIFFRACTION3(chain 'D' and resid 3 through 19)D3 - 19

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