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- PDB-5h9v: Crystal structure of Regnase PIN domain, form I -

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Basic information

Entry
Database: PDB / ID: 5h9v
TitleCrystal structure of Regnase PIN domain, form I
ComponentsRibonuclease ZC3H12A
KeywordsHYDROLASE / RNase
Function / homology
Function and homology information


immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / negative regulation of muscle cell apoptotic process / RNA exonuclease activity / miRNA catabolic process / rough endoplasmic reticulum membrane / positive regulation of mRNA catabolic process / negative regulation of T-helper 17 cell differentiation / host-mediated suppression of viral genome replication ...immune response-activating signaling pathway / positive regulation of miRNA catabolic process / positive regulation of protein deubiquitination / negative regulation of muscle cell apoptotic process / RNA exonuclease activity / miRNA catabolic process / rough endoplasmic reticulum membrane / positive regulation of mRNA catabolic process / negative regulation of T-helper 17 cell differentiation / host-mediated suppression of viral genome replication / cellular response to sodium arsenite / negative regulation of cardiac muscle contraction / cellular response to ionomycin / 3'-UTR-mediated mRNA destabilization / nuclease activity / positive regulation of lipid storage / negative regulation of nitric oxide biosynthetic process / cellular response to chemokine / mRNA 3'-UTR AU-rich region binding / positive regulation of p38MAPK cascade / negative regulation of non-canonical NF-kappaB signal transduction / miRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of interleukin-1 beta production / mRNA catabolic process / negative regulation of protein phosphorylation / protein complex oligomerization / negative regulation of type II interferon production / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / cellular response to interleukin-1 / protein deubiquitination / positive regulation of execution phase of apoptosis / positive regulation of fat cell differentiation / cellular response to glucose starvation / rough endoplasmic reticulum / positive regulation of defense response to virus by host / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / positive regulation of autophagy / positive regulation of endothelial cell migration / RNA endonuclease activity / mRNA 3'-UTR binding / P-body / cellular response to virus / positive regulation of protein import into nucleus / RNA stem-loop binding / positive regulation of reactive oxygen species metabolic process / positive regulation of angiogenesis / cellular response to tumor necrosis factor / nervous system development / T cell receptor signaling pathway / ribosome binding / cellular response to lipopolysaccharide / cellular response to oxidative stress / angiogenesis / Hydrolases; Acting on ester bonds / cysteine-type deubiquitinase activity / 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 / zinc ion binding / nucleoplasm / nucleus / 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 / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / Rossmann fold - #11980 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease ZC3H12A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsYokogawa, M. / Tsushima, T. / Adachi, W. / Noda, N.N. / Inagaki, F.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS Japan
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Authors: Yokogawa, M. / Tsushima, T. / Noda, N.N. / Kumeta, H. / Enokizono, Y. / Yamashita, K. / Standley, D.M. / Takeuchi, O. / Akira, S. / Inagaki, F.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,9638
Polymers98,8714
Non-polymers924
Water00
1
A: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7412
Polymers24,7181
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7412
Polymers24,7181
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7412
Polymers24,7181
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease ZC3H12A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7412
Polymers24,7181
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.370, 113.370, 187.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A134 - 295
2115B134 - 295
3115C134 - 295
4115D134 - 295

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999914, -0.002978, 0.012755), (0.012885, 0.048884, -0.998721), (0.002351, 0.9988, 0.048918)27.9583, 78.08489, -18.89202
3given(-0.515416, -0.856499, 0.027507), (0.710309, -0.444959, -0.545411), (0.479383, -0.261575, 0.837718)-25.98668, 90.10177, 58.27846
4given(-0.499383, -0.8663, 0.01182), (0.505407, -0.280209, 0.816117), (-0.70369, 0.413529, 0.577767)-53.4827, 77.18489, -9.2304

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Components

#1: Protein
Ribonuclease ZC3H12A / Regnase-1 / MCP-induced protein 1 / Zinc finger CCCH domain-containing protein 12A


Mass: 24717.869 Da / Num. of mol.: 4 / Fragment: PIN domain, UNP residues 134-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3h12a, Mcpip, Mcpip1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5D1E7, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1 M (NH4)2HPO4, 200 mM NaCl, 100 mM sodium citrate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97899, 0.97928, 0.96405
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979281
30.964051
ReflectionResolution: 2.75→47.49 Å / Num. obs: 33467 / % possible obs: 90.5 % / Redundancy: 7.9 % / Net I/σ(I): 22.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.75→47.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 25.849 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22642 1656 5 %RANDOM
Rwork0.18924 ---
obs0.1911 31767 90.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.716 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å2-2.39 Å20 Å2
2---2.39 Å20 Å2
3---7.74 Å2
Refinement stepCycle: 1 / Resolution: 2.75→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 0 4 0 5289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195412
X-RAY DIFFRACTIONr_bond_other_d0.0010.025228
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.9667311
X-RAY DIFFRACTIONr_angle_other_deg0.85312006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73422.626278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25115926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9811563
X-RAY DIFFRACTIONr_chiral_restr0.0890.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2163.392567
X-RAY DIFFRACTIONr_mcbond_other2.2163.392566
X-RAY DIFFRACTIONr_mcangle_it3.6125.0793200
X-RAY DIFFRACTIONr_mcangle_other3.6125.0793201
X-RAY DIFFRACTIONr_scbond_it2.7123.7712845
X-RAY DIFFRACTIONr_scbond_other2.7123.772846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.525.514112
X-RAY DIFFRACTIONr_long_range_B_refined6.50427.1326210
X-RAY DIFFRACTIONr_long_range_B_other6.50427.1336211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A905medium positional0.530.5
B905medium positional0.30.5
C905medium positional0.280.5
D905medium positional0.270.5
A1612loose positional0.945
B1612loose positional0.715
C1612loose positional0.75
D1612loose positional0.645
A905medium thermal6.032
B905medium thermal3.932
C905medium thermal5.322
D905medium thermal4.062
A1612loose thermal7.0910
B1612loose thermal5.4110
C1612loose thermal6.7810
D1612loose thermal5.3910
LS refinement shellResolution: 2.748→2.819 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 66 -
Rwork0.289 1417 -
obs--55.38 %
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)
110.8875-0.0875-2.28054.39770.31133.25070.0794-0.99020.5142-0.14940.1540.0826-0.42160.1881-0.23340.0742-0.07160.05880.5715-0.05470.4463-41.459549.565934.0318
210.1457-1.54991.02372.9722-1.01034.94390.04211.51210.1167-0.2148-0.0866-0.139-0.01130.12060.04450.05370.07730.10710.67550.05370.3918-70.151951.557830.3242
37.13731.95410.22674.35560.36592.6596-0.38470.6622-0.2179-0.76890.3956-0.22580.07660.1841-0.01090.4824-0.32220.08850.2862-0.13360.5225-32.254337.61461.3966
44.91682.27340.89558.92651.82773.79710.3092-0.2027-0.05250.8211-0.3644-0.35750.2237-0.03040.05520.6198-0.2862-0.01160.2342-0.03330.403-50.30815.20972.6666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 294
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B134 - 296
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C134 - 295
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D134 - 295
8X-RAY DIFFRACTION4D401

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