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- PDB-6nf0: Nocturnin with bound NADPH substrate -

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Basic information

Entry
Database: PDB / ID: 6nf0
TitleNocturnin with bound NADPH substrate
ComponentsNocturnin
KeywordsHYDROLASE / Circadian clock / metabolism
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 / negative regulation of osteoblast differentiation ...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 / negative regulation of osteoblast differentiation / positive regulation of fat cell 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 / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Nocturnin, deadenylase domain / : / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
Chem-NDP / Nocturnin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEstrella, M.A. / Du, J. / Korennykh, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM110161 United States
Other private1013579 United States
CitationJournal: Nat Commun / Year: 2019
Title: The metabolites NADP+and NADPH are the targets of the circadian protein Nocturnin (Curled).
Authors: Estrella, M.A. / Du, J. / Chen, L. / Rath, S. / Prangley, E. / Chitrakar, A. / Aoki, T. / Schedl, P. / Rabinowitz, J. / Korennykh, A.
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Nocturnin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2763
Polymers35,4901
Non-polymers7852
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Enzymatic assays.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.888, 62.888, 153.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 35490.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOCT, CCR4, CCRN4L, NOC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UK39, poly(A)-specific ribonuclease
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Co-crystals were grown using the hanging drop vapor diffusion method by mixing the crystallization complex 1:1 with reservoir solution (100 mM HEPES pH 7.5, 10% (v/v) Isopropanol, 50 mM ...Details: Co-crystals were grown using the hanging drop vapor diffusion method by mixing the crystallization complex 1:1 with reservoir solution (100 mM HEPES pH 7.5, 10% (v/v) Isopropanol, 50 mM Sodium Acetate, and 12% (w/v) PEG 4,000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.05→29.1 Å / Num. obs: 10499 / % possible obs: 93.2 % / Redundancy: 12.65 % / CC1/2: 0.9992 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.034 / Rrim(I) all: 0.123 / Net I/σ(I): 14.277
Reflection shellResolution: 2.053→2.335 Å / Redundancy: 11.88 % / Rmerge(I) obs: 1.471 / Num. unique obs: 580 / CC1/2: 0.7604 / Rpim(I) all: 0.443 / Rrim(I) all: 1.538 / % possible all: 82.39

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MAL

6mal


Resolution: 2.7→29.099 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.27
RfactorNum. reflection% reflection
Rfree0.264 417 4.92 %
Rwork0.2063 --
obs0.2092 8470 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 49 18 2429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052480
X-RAY DIFFRACTIONf_angle_d0.8023381
X-RAY DIFFRACTIONf_dihedral_angle_d21.5982046
X-RAY DIFFRACTIONf_chiral_restr0.052370
X-RAY DIFFRACTIONf_plane_restr0.005435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.09040.27381140.23282236X-RAY DIFFRACTION81
3.0904-3.89210.32591340.20712843X-RAY DIFFRACTION100
3.8921-29.10110.23071690.19762974X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.3453 Å / Origin y: -29.8296 Å / Origin z: -9.5235 Å
111213212223313233
T0.1956 Å20.0419 Å20.0725 Å2-0.2028 Å2-0.0188 Å2--0.0601 Å2
L3.5448 °2-0.7894 °20.4388 °2-3.9838 °20.1507 °2--7.9647 °2
S-0.1988 Å °-0.0776 Å °-0.1251 Å °-0.0696 Å °0.0209 Å °-0.2538 Å °0.2847 Å °0.7918 Å °0.0718 Å °
Refinement TLS groupSelection details: all

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