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- PDB-5lon: Structure of /K. lactis/ Dcp1-Dcp2 decapping complex. -

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Basic information

Entry
Database: PDB / ID: 5lon
TitleStructure of /K. lactis/ Dcp1-Dcp2 decapping complex.
Components
  • KLLA0E01827p
  • KLLA0F23980p
KeywordsRNA BINDING PROTEIN / RNA decay / multiprotein complex
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / enzyme activator activity / P-body / manganese ion binding / mRNA binding / RNA binding
Similarity search - Function
mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
KLLA0F23980p / KLLA0E01827p
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCharenton, C. / Taverniti, V. / Gaudon-Plesse, C. / Back, R. / Seraphin, B. / Graille, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV800902 France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to m(7)GDP and its Edc3 activator.
Authors: Charenton, C. / Taverniti, V. / Gaudon-Plesse, C. / Back, R. / Seraphin, B. / Graille, M.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 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
A: KLLA0F23980p
B: KLLA0E01827p


Theoretical massNumber of molelcules
Total (without water)54,5652
Polymers54,5652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-17 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.685, 216.685, 216.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein KLLA0F23980p


Mass: 32634.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: KLLA0_F23980g / Production host: Escherichia coli (E. coli) / Variant (production host): Codon+ / References: UniProt: Q6CIU1
#2: Protein KLLA0E01827p


Mass: 21929.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: KLLA0_E01827g / Production host: Escherichia coli (E. coli) / Variant (production host): Codon+ / References: UniProt: Q6CPV9

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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: 4 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M ammonium sulfate ; 0.1M tri- sodium citrate pH 5.6 ; 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→48.45 Å / Num. obs: 11272 / % possible obs: 99.9 % / Redundancy: 78.7 % / Biso Wilson estimate: 114.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rsym value: 0.257 / Net I/σ(I): 18.7
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 78.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2 / CC1/2: 0.442 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LOP

5lop


Resolution: 3.5→48.45 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.866 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.577
RfactorNum. reflection% reflectionSelection details
Rfree0.312 543 4.82 %RANDOM
Rwork0.25 ---
obs0.253 11272 100 %-
Displacement parametersBiso mean: 210.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.64 Å
Refinement stepCycle: LAST / Resolution: 3.5→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 5 0 3244
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013319HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184494HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1168SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes456HARMONIC5
X-RAY DIFFRACTIONt_it3319HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion25.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion427SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3667SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 129 4.93 %
Rwork0.271 2486 -
all0.274 2615 -
obs--100 %
Refinement TLS params.

L22: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°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)
12.2663-1.1656-1.192-0.13786.98050.094-0.0979-1.08850.1162-0.2764-0.05241.0885-0.44480.18240.4936-0.13740.304-0.3494-0.03190.6079-81.08215.4393-46.1654
21.3562.66671.8906-0.08790.69110.2649-0.2585-0.1227-0.0363-0.29340.2957-0.046-0.18380.02850.08730.01440.23950.08-0.0180.3755-57.310524.6888-39.3108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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