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- PDB-6am0: Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping comp... -

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Basic information

Entry
Database: PDB / ID: 6am0
TitleCrystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog
Components
  • KLLA0A01474p
  • KLLA0A11308p
  • KLLA0E01827p
  • KLLA0F23980p
KeywordsTRANSLATION / mRNA decay / decapping / Nudix / nucleotide analog
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 / P-body assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / enzyme activator activity / P-body / mRNA processing / manganese ion binding / mRNA binding / RNA binding
Similarity search - Function
Dcp2, box A domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily ...Dcp2, box A domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / 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. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / 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 / Arc Repressor Mutant, subunit A / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6VQ / KLLA0F23980p / KLLA0E01827p / Enhancer of mRNA-decapping protein 3 / KLLA0A01474p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsMugridge, J.S. / Gross, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM078360 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105313 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis.
Authors: Mugridge, J.S. / Tibble, R.W. / Ziemniak, M. / Jemielity, J. / Gross, J.D.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: KLLA0F23980p
B: KLLA0E01827p
C: KLLA0A01474p
D: KLLA0A11308p
E: KLLA0F23980p
F: KLLA0E01827p
G: KLLA0A01474p
H: KLLA0A11308p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,81711
Polymers127,9318
Non-polymers1,8853
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17640 Å2
ΔGint-109 kcal/mol
Surface area53130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.260, 83.250, 104.300
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 6 molecules AEBFDH

#1: Protein KLLA0F23980p


Mass: 31804.855 Da / Num. of mol.: 2 / Fragment: unp residues 1-275 / Mutation: E152Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_F23980g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: Q6CIU1
#2: Protein KLLA0E01827p


Mass: 22073.959 Da / Num. of mol.: 2 / Fragment: unp residues 1-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_E01827g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPV9
#4: Protein KLLA0A11308p


Mass: 7331.633 Da / Num. of mol.: 2 / Fragment: unp residues 1-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_A11308g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: Q6CX48

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Protein/peptide , 1 types, 2 molecules CG

#3: Protein/peptide KLLA0A01474p


Mass: 2755.126 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CYC5

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-6VQ / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 930.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H34N10O19P4S2

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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: 2.96 Å3/Da / Density % sol: 58 % / Description: rhombohedral blocks, ~40-80 microns.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 4mg/mL Kl Dcp1/Dcp2/Edc3, 1mM Edc1 peptide, 6mM substrate analog, 10mM magnsium chloride. Well solution: 0.22M magnesium chloride, 0.03M EDTA, 8% PEG 8000. Procedure: 250nL ...Details: Protein solution: 4mg/mL Kl Dcp1/Dcp2/Edc3, 1mM Edc1 peptide, 6mM substrate analog, 10mM magnsium chloride. Well solution: 0.22M magnesium chloride, 0.03M EDTA, 8% PEG 8000. Procedure: 250nL protein solution + 250nL well solution + 50nL 1:10000 seed stock. Set up at RT, grow crystals at 4C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2017
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 68126 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.82
Reflection shellResolution: 2.84→3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Blu-Icedata collection
XDSNov 1, 2016data reduction
XSCALENov 1, 2016data scaling
PHASER2.5.7phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LOP

5lop


Resolution: 2.84→45.96 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1998 5.66 %Random
Rwork0.225 ---
obs0.227 35286 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8484 0 115 0 8599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038796
X-RAY DIFFRACTIONf_angle_d0.72111927
X-RAY DIFFRACTIONf_dihedral_angle_d17.8395297
X-RAY DIFFRACTIONf_chiral_restr0.0441338
X-RAY DIFFRACTIONf_plane_restr0.0051484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.9110.42691370.36832339X-RAY DIFFRACTION100
2.911-2.98970.36081510.33132373X-RAY DIFFRACTION100
2.9897-3.07770.34761370.31112388X-RAY DIFFRACTION100
3.0777-3.1770.32741400.30682368X-RAY DIFFRACTION100
3.177-3.29050.36721400.2952336X-RAY DIFFRACTION100
3.2905-3.42220.29551450.27552382X-RAY DIFFRACTION100
3.4222-3.57790.34731380.26692401X-RAY DIFFRACTION100
3.5779-3.76640.29211430.2522338X-RAY DIFFRACTION100
3.7664-4.00230.25631450.23732396X-RAY DIFFRACTION100
4.0023-4.31110.26971430.20872389X-RAY DIFFRACTION100
4.3111-4.74460.20561450.19652356X-RAY DIFFRACTION99
4.7446-5.43020.2381430.19672388X-RAY DIFFRACTION100
5.4302-6.83780.22851450.23382386X-RAY DIFFRACTION99
6.8378-45.96150.18371460.18782448X-RAY DIFFRACTION99
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)
11.1137-0.22580.14910.7305-0.7842.6311-0.3755-1.2619-0.41391.75630.9689-0.0359-0.4281-0.65361.22454.49640.4789-0.78591.88020.32231.4752-27.889534.866933.3957
25.29371.99780.57753.494.57627.8882-1.2378-0.4172-0.9922-1.378-0.10980.0657-3.6479-1.9144-0.45082.70490.0227-0.12410.87450.21971.1398-16.224829.340344.8682
31.37761.1931.01971.14821.13211.2106-1.17320.549-0.53552.06191.3048-0.5194-1.02292.1326-0.04374.2141-0.5285-0.79620.91190.46261.6611-20.188137.214238.5442
42.0317-0.0822-0.72410.0203-0.04350.2812-0.40590.7770.64590.01780.4094-1.1455-1.8041-0.181-0.00093.33680.17050.23341.13820.11981.7626-15.703137.941341.2083
52.6215-0.34272.15870.044-0.29741.781-1.98211.03181.70532.87861.3513.0776-2.49092.3944-0.10781.82510.36620.91381.0003-0.31413.0916-10.761935.625436.8067
63.74170.74072.23576.58367.57139.2755-1.9420.144-0.41260.4455-0.0687-1.2521-0.6448-1.8913-2.57623.1476-0.04490.7450.40370.80081.0806-17.468725.28239.9337
75.7785-1.86493.08510.8779-0.80621.7914-0.24120.78560.3250.5059-0.4024-0.2202-0.0884-0.741-4.17582.92571.28850.12232.29251.01080.2939-31.470733.479742.5326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'H' AND (RESID 2 THROUGH 7 )
2X-RAY DIFFRACTION2CHAIN 'H' AND (RESID 8 THROUGH 18 )
3X-RAY DIFFRACTION3CHAIN 'H' AND (RESID 19 THROUGH 26 )
4X-RAY DIFFRACTION4CHAIN 'H' AND (RESID 27 THROUGH 45 )
5X-RAY DIFFRACTION5CHAIN 'H' AND (RESID 46 THROUGH 53 )
6X-RAY DIFFRACTION6CHAIN 'H' AND (RESID 54 THROUGH 59 )
7X-RAY DIFFRACTION7CHAIN 'H' AND (RESID 60 THROUGH 64 )

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