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- PDB-8rdd: Crystal structure of Saccharomyces cerevisiae Nmd4 protein involv... -

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Basic information

Entry
Database: PDB / ID: 8rdd
TitleCrystal structure of Saccharomyces cerevisiae Nmd4 protein involved in nonsense mediated mRNA decay
ComponentsNonsense-mediated decay protein 4
KeywordsRNA BINDING PROTEIN / Nonsense-mediated mRNA decay / PIN domain
Function / homologyLarge family of predicted nucleotide-binding domains / PIN domain / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nucleus / cytoplasm / ACETIC ACID / Nonsense-mediated decay protein 4
Function and homology information
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsBarbarin-Bocahu, I. / Graille, M.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0003-04 France
Centre National de la Recherche Scientifique (CNRS) France
Ecole polytechnique France
CitationJournal: To Be Published
Title: Structure of a yeast protein
Authors: Barbarin-Bocahu, I. / Ulryck, N. / Rigobert, A. / Ruiz Gutierrez, N. / Decourty, L. / Raji, M. / Garkhal, B. / Le Hir, H. / Saveanu, C. / Graille, M.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nonsense-mediated decay protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8394
Polymers19,6271
Non-polymers2123
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-1 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.371, 80.371, 94.134
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nonsense-mediated decay protein 4


Mass: 19626.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: NMD4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q12129
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Na citrate, 0.1 M Na cacodylate pH 6.5, 0.2 M lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40.2 Å / Num. obs: 31899 / % possible obs: 95.7 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rpim(I) all: 0.0015 / Net I/σ(I): 25.7
Reflection shellResolution: 1.8→1.853 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1598 / CC1/2: 0.608 / Rpim(I) all: 0.58

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→40.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.089 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 1580 -RANDOM
Rwork0.1811 ---
obs0.1816 31899 95.7 %-
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.3052 Å20 Å20 Å2
2--0.3052 Å20 Å2
3----0.6104 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.796→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 14 208 1556
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091404HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.861897HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d509SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes242HARMONIC5
X-RAY DIFFRACTIONt_it1404HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion186SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1357SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion16.63
LS refinement shellResolution: 1.8→1.82 Å
RfactorNum. reflection% reflection
Rfree0.2787 27 -
Rwork0.2918 --
obs0.2912 638 42.38 %
Refinement TLS params.Origin x: -29.5393 Å / Origin y: 24.8888 Å / Origin z: -29.0679 Å
111213212223313233
T-0.0018 Å20.0067 Å20.0015 Å2--0.0476 Å2-0.0004 Å2---0.0381 Å2
L1.3342 °2-0.1481 °2-0.2783 °2-0.8424 °20.3396 °2--1.3547 °2
S0.0436 Å °0.1049 Å °0.0369 Å °0.1049 Å °0.0042 Å °-0.0507 Å °0.0369 Å °-0.0507 Å °-0.0478 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 164
2X-RAY DIFFRACTION1{ B|* }B201 - 206

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