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- PDB-6bt2: Structure of the human Nocturnin catalytic domain with bound sulf... -

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Basic information

Entry
Database: PDB / ID: 6bt2
TitleStructure of the human Nocturnin catalytic domain with bound sulfate anion
ComponentsNocturnin
KeywordsHydrolase / RNA BINDING PROTEIN / EEP superfamily
Function / homology
Function and homology information


nocturnin / NADP phosphatase activity / NADPH phosphatase activity / poly(A)-specific ribonuclease activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / NADP metabolic process / P-body assembly / : / mRNA stabilization / regulation of embryonic development ...nocturnin / NADP phosphatase activity / NADPH phosphatase activity / poly(A)-specific ribonuclease activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / NADP metabolic process / P-body assembly / : / mRNA stabilization / regulation of embryonic development / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / BMAL1:CLOCK,NPAS2 activates circadian gene expression / P-body / circadian regulation of gene expression / regulation of circadian rhythm / 3'-5'-RNA exonuclease activity / response to lipopolysaccharide / transcription by RNA polymerase II / negative regulation of gene expression / mRNA binding / perinuclear region of cytoplasm / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nocturnin, deadenylase domain / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.411 Å
AuthorsAbshire, E.T. / Chasseur, J. / Del Rizzo, P. / Trievel, R.
Funding support United States, 4items
OrganizationGrant numberCountry
Edward Mallinckrodt Jr. Foundation United States
Michigan Nutrition and Obesity Research Center United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008597 United States
American Heart Association16PRE26700002 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells.
Authors: T Abshire, E. / Chasseur, J. / Bohn, J.A. / Del Rizzo, P.A. / Freddolino, P.L. / Goldstrohm, A.C. / Trievel, R.C.
History
DepositionDec 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_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 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nocturnin
B: Nocturnin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6528
Polymers71,3632
Non-polymers2896
Water4,035224
1
A: Nocturnin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8264
Polymers35,6811
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nocturnin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8264
Polymers35,6811
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.004, 69.437, 153.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nocturnin / / Carbon catabolite repression 4-like protein / Circadian deadenylase NOC


Mass: 35681.305 Da / Num. of mol.: 2 / Fragment: residues 120-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOCT, CCR4, CCRN4L, NOC / Plasmid: pSumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta 2 / References: UniProt: Q9UK39, poly(A)-specific ribonuclease
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Adenosine 5' Monophosphate, Magnesium Chloride, HEPES, Isopropanol, Sodium Acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→48.2 Å / Num. obs: 26012 / % possible obs: 98.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.11 / Net I/σ(I): 13.82
Reflection shellResolution: 2.411→2.419 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.461 / CC1/2: 0.895 / Rrim(I) all: 0.503 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished structure

Resolution: 2.411→48.231 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 1301 5.01 %
Rwork0.1612 --
obs0.1644 25994 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.411→48.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 14 224 4506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084401
X-RAY DIFFRACTIONf_angle_d1.025999
X-RAY DIFFRACTIONf_dihedral_angle_d13.9061555
X-RAY DIFFRACTIONf_chiral_restr0.041667
X-RAY DIFFRACTIONf_plane_restr0.004772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4113-2.50780.34741310.23122469X-RAY DIFFRACTION91
2.5078-2.6220.27251400.20782686X-RAY DIFFRACTION99
2.622-2.76020.25681460.18312751X-RAY DIFFRACTION100
2.7602-2.93310.27141430.17652732X-RAY DIFFRACTION100
2.9331-3.15950.22511460.17292755X-RAY DIFFRACTION100
3.1595-3.47740.22741450.15262760X-RAY DIFFRACTION100
3.4774-3.98040.19841470.14542778X-RAY DIFFRACTION100
3.9804-5.0140.17891470.12472813X-RAY DIFFRACTION100
5.014-48.24040.22881560.17382949X-RAY DIFFRACTION100
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)
18.4163-1.2419-0.92297.78026.01987.46890.27951.49760.9693-1.1821-0.8149-0.1125-0.6359-0.41540.46840.5998-0.01190.03370.55720.14450.330314.8477-0.3232-44.4052
22.82452.17781.02491.77021.38845.29770.17980.08920.2991-0.0413-0.14410.3306-0.4797-0.3792-0.1550.39670.04370.00690.2570.08470.2557.3742-2.5863-29.2717
35.4968-0.0749-2.93985.7015-1.75547.0250.0130.51420.393-0.24760.07070.2488-0.5109-0.7243-0.07680.36120.0213-0.06190.34560.00370.19393.3986-6.5081-32.7158
42.6139-0.5815-0.44542.842.01837.9382-0.01520.3441-0.0576-0.1262-0.10330.23250.3247-0.10120.09460.3106-0.04230.00370.22350.04430.20847.9855-16.6327-25.9232
53.1660.54571.63455.26083.44678.9474-0.10850.1954-0.3147-0.05140.0896-0.28010.27160.833-0.01310.22580.01410.05610.33180.0530.228120.7103-15.5161-23.3492
65.34472.90480.44399.14663.39664.60950.09850.0484-0.26620.2894-0.1734-0.83170.25530.7841-0.02120.30950.0798-0.00060.44540.09580.235125.9902-12.3702-25.6924
72.75390.43940.50956.5517-5.02958.1892-0.07580.53430.2249-0.3638-0.4445-0.8751-0.14781.1480.54180.38470.03310.08850.6280.12640.381528.7776-5.2271-33.6177
82.99010.0567-0.42892.63781.02054.01030.09810.40220.1895-0.3607-0.08890.064-0.36230.0553-0.02560.38020.00910.020.41470.12190.271918.6676-4.1091-34.8911
92.64231.0214-1.25692.9705-0.46356.03730.07330.0740.1699-0.1220.01420.1075-0.1181-0.1655-0.10080.2240.0296-0.02190.222-0.01260.2167-8.5594-23.2899-7.0081
102.63310.73280.66542.4251.24594.134-0.0420.0608-0.3032-0.07510.1117-0.23950.46730.1542-0.09270.3810.07880.02070.2318-0.03080.2624-0.238-38.1998-12.8319
115.3911-0.6536-1.41989.8447-4.34012.66990.03060.3045-0.27550.03570.16320.32931.0408-1.2562-0.12090.6543-0.18540.02770.5595-0.01230.2997-18.1387-41.3009-7.4089
125.2896-3.89460.68356.9062-0.39784.1259-0.1528-0.2464-0.36350.14150.17070.28490.4906-0.1545-0.03010.2944-0.0790.03010.24790.03160.2193-10.5671-36.2254-2.1631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 121 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 202 )
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 311 )
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 339 )
7X-RAY DIFFRACTION7chain 'A' and (resid 340 through 361 )
8X-RAY DIFFRACTION8chain 'A' and (resid 362 through 425 )
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 234 )
10X-RAY DIFFRACTION10chain 'B' and (resid 235 through 351 )
11X-RAY DIFFRACTION11chain 'B' and (resid 352 through 376 )
12X-RAY DIFFRACTION12chain 'B' and (resid 377 through 425 )

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