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- PDB-5lop: Structure of the active form of /K. lactis/ Dcp1-Dcp2-Edc3 decapp... -

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Basic information

Entry
Database: PDB / ID: 5lop
TitleStructure of the active form of /K. lactis/ Dcp1-Dcp2-Edc3 decapping complex bound to m7GDP
Components
  • KLLA0A11308p
  • KLLA0E01827p
  • KLLA0F23980p
KeywordsRNA BINDING PROTEIN / RNA decay / multiprotein complex
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / 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
FDF domain / DFDF domain / DFDF domain profile. / FDF / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. ...FDF domain / DFDF domain / DFDF domain profile. / FDF / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / 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 / : / Sm domain profile. / NUDIX hydrolase, conserved site / Nudix box signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / NUDIX domain / PH-domain like / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / KLLA0F23980p / KLLA0E01827p / Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 2.0May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KLLA0F23980p
B: KLLA0E01827p
C: KLLA0A11308p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4277
Polymers61,8963
Non-polymers5314
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-67 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.810, 219.810, 74.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 3 types, 3 molecules ABC

#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
#3: Protein KLLA0A11308p


Mass: 7331.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: KLLA0_A11308g / Production host: Escherichia coli (E. coli) / Variant (production host): Codon+ / References: UniProt: Q6CX48

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Non-polymers , 3 types, 11 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.18 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 400, 100 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0725 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0725 Å / Relative weight: 1
ReflectionResolution: 3.5→48.2 Å / Num. obs: 13907 / % possible obs: 99.8 % / Redundancy: 21.2 % / Biso Wilson estimate: 205.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.026 / Rsym value: 0.085 / Net I/σ(I): 19.4
Reflection shellResolution: 3.5→3.82 Å / Redundancy: 21.2 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.362 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.5→48.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.497
RfactorNum. reflection% reflectionSelection details
Rfree0.266 697 5.02 %RANDOM
Rwork0.2 ---
obs0.203 13889 99.8 %-
Displacement parametersBiso mean: 230.45 Å2
Baniso -1Baniso -2Baniso -3
1--17.2818 Å20 Å20 Å2
2---17.2818 Å20 Å2
3---34.5636 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: 1 / Resolution: 3.5→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 32 7 4077
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014158HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.315627HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1481SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it4158HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion25.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion534SEMIHARMONIC5
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_contact4881SEMIHARMONIC4
LS refinement shellResolution: 3.49→3.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.311 141 5.09 %
Rwork0.25 2629 -
all0.253 2770 -
obs--99.25 %
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)
12.9985-2.8691-1.37453.75571.99063.8131-0.3014-0.3506-0.3840.50250.29940.46480.56860.37180.002-0.21260.02670.3141-0.2333-0.1696-0.250555.313632.6685.0229
212.0119-0.1491-4.00718.15182.12457.261-0.1286-0.26890.16560.7481-0.3989-0.604-0.38610.40690.52750.1139-0.4030.1204-0.1176-0.2815-0.108360.845464.64116.2651
36.4264-1.1501-1.45740.5933.23578.174-0.0654-0.14470.23650.216-0.01820.063-0.12340.14240.08350.07270.2577-0.14720.0258-0.2356-0.3288102.244612.97576.7455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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