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- PDB-5kq1: Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapien... -

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Basic information

Entry
Database: PDB / ID: 5kq1
TitleCrystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2
Components
  • Proline-rich nuclear receptor coactivator 2
  • mRNA decapping complex subunit 2
  • mRNA-decapping enzyme subunit 1
KeywordsHYDROLASE / decapping mRNA decay Nudix cap analog
Function / homology
Function and homology information


mRNA phosphatase activator activity / : / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding ...mRNA phosphatase activator activity / : / RNA decapping complex / mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / P-body / mRNA processing / cytoplasmic stress granule / manganese ion binding / single-stranded RNA binding / Golgi apparatus / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proline-rich nuclear receptor coactivator 1/2 / Proline-rich nuclear receptor coactivator motif / 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 ...Proline-rich nuclear receptor coactivator 1/2 / Proline-rich nuclear receptor coactivator motif / 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) / 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
mRNA decapping complex subunit 2 / Proline-rich nuclear receptor coactivator 2 / mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.002 Å
AuthorsMugridge, J.S. / Ziemniak, M. / Jemielity, J. / 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.Struct.Mol.Biol. / Year: 2016
Title: Structural basis of mRNA-cap recognition by Dcp1-Dcp2.
Authors: Mugridge, J.S. / Ziemniak, M. / Jemielity, J. / Gross, J.D.
History
DepositionJul 5, 2016Deposition site: RCSB / Processing site: RCSB
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 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700 SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA-decapping enzyme subunit 1
C: Proline-rich nuclear receptor coactivator 2
B: mRNA decapping complex subunit 2
D: mRNA-decapping enzyme subunit 1
F: Proline-rich nuclear receptor coactivator 2
E: mRNA decapping complex subunit 2


Theoretical massNumber of molelcules
Total (without water)95,2936
Polymers95,2936
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-50 kcal/mol
Surface area38260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.622, 118.727, 93.174
Angle α, β, γ (deg.)90.00, 102.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein mRNA-decapping enzyme subunit 1


Mass: 15335.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: dcp1, SPBC3B9.21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: Q9P805
#2: Protein/peptide Proline-rich nuclear receptor coactivator 2


Mass: 3365.766 Da / Num. of mol.: 2 / Fragment: unp residues 72-102
Source method: isolated from a genetically manipulated source
Details: C-terminus of PNRC2 is linked to N-terminus of Dcp2 by GGGGS linker
Source: (gene. exp.) Homo sapiens (human) / Gene: PNRC2, HSPC208 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: Q9NPJ4
#3: Protein mRNA decapping complex subunit 2


Mass: 28945.359 Da / Num. of mol.: 2 / Fragment: unp residues 1-244
Source method: isolated from a genetically manipulated source
Details: GGGGS linker at the N-terminus of Dcp2 is connected to the C-terminus of PNRC2
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: dcp2, SPAC19A8.12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: O13828, Hydrolases

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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: 2.58 Å3/Da / Density % sol: 52.37 % / Description: Plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 150 mM trilithium citrate, 13% PEG 3350, 0.1% mellitic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19125 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 86.15 Å2 / Rmerge(I) obs: 0.106 / Net I/av σ(I): 24.176 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3-3.053.40.7450.796191.9
3.05-3.113.50.680.807196.6
3.11-3.173.60.5860.839197.6
3.17-3.233.60.5560.882199
3.23-3.33.70.4290.92199.7
3.3-3.383.80.3370.9441100
3.38-3.463.80.2880.9581100
3.46-3.563.80.2330.9581100
3.56-3.663.80.1990.9671100
3.66-3.783.80.1730.971100
3.78-3.913.80.1540.9761100
3.91-4.073.80.1430.9711100
4.07-4.263.70.1290.9741100
4.26-4.483.80.120.9661100
4.48-4.763.80.1150.9761100
4.76-5.133.70.0950.9841100
5.13-5.643.70.0930.9851100
5.64-6.463.60.0820.986199.9
6.46-8.133.80.0720.993199.9
8.13-503.70.0610.99196.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Blu-Icedata collection
HKL-2000v708cdata reduction
HKL-2000v708cdata scaling
PHASERphasing
Cootv0.8.2model building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QKM

2qkm


Resolution: 3.002→44.494 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 920 4.82 %
Rwork0.2101 --
obs0.212 19093 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.002→44.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6274 0 0 0 6274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036440
X-RAY DIFFRACTIONf_angle_d0.6168713
X-RAY DIFFRACTIONf_dihedral_angle_d19.3393868
X-RAY DIFFRACTIONf_chiral_restr0.046935
X-RAY DIFFRACTIONf_plane_restr0.0041112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0022-3.16050.38151110.33722376X-RAY DIFFRACTION91
3.1605-3.35840.3471600.30592601X-RAY DIFFRACTION99
3.3584-3.61760.28851320.23472619X-RAY DIFFRACTION100
3.6176-3.98150.25331230.21632640X-RAY DIFFRACTION100
3.9815-4.55710.23731170.1922667X-RAY DIFFRACTION100
4.5571-5.73960.22011640.18772611X-RAY DIFFRACTION100
5.7396-44.49890.2161130.18822659X-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)
13.1436-0.2735-0.08522.4478-0.54412.31480.5819-0.31570.49850.7207-0.1258-1.2471-0.68680.2333-0.1270.9364-0.0585-0.18370.6478-0.0490.94111.475910.44725.0538
27.1827-1.72396.38928.7913-1.70417.20631.785-0.273-0.1251-0.4626-0.20640.84391.0428-0.9349-0.3510.5034-0.19710.19920.43980.02830.8105-0.99516.67310.3739
35.1634-0.34724.8427.4785-1.69314.61710.73730.5985-1.0353-1.51660.0586-0.38690.37660.2609-0.74980.97090.1228-0.13250.5925-0.1030.8090.70537.17836.6153
43.2154-3.1338-0.52972.94650.31612.6070.0719-0.12690.2403-0.7533-0.4742-0.8967-0.99660.88520.55111.00260.06930.0380.59870.00010.94318.74969.686212.1853
58.5558-0.81150.72051.0192-1.69074.50420.33830.33821.8781-0.1612-0.7977-0.4743-1.4391-0.9270.13710.62360.3565-0.11040.628-0.08560.9779-0.787118.00688.1562
62.95721.832-2.88727.5191-2.70533.22450.22250.00870.8711-0.71450.14030.24020.13161.0873-0.27481.13970.0556-0.2190.7762-0.00461.0273-3.192913.51864.6281
78.3156-0.0135-1.13774.0274-2.15932.25190.2584-0.4271-0.85580.6766-0.66360.83281.768-0.6027-0.24781.2165-0.0507-0.080.69420.06130.8011-5.20855.736911.6681
84.54175.1311-3.72985.7461-4.22993.08730.3398-1.49231.50393.0908-0.30161.3824-0.8722-0.1371-0.29031.16580.0476-0.14270.9929-0.14381.007-5.970816.603418.0182
98.91776.72364.31859.86432.30362.35040.869-0.0753-1.1722-1.83270.67772.58251.1256-0.5338-0.79081.4659-0.1091-0.01270.83210.13520.9112-9.96573.76073.7886
103.4923-0.5991-3.90580.93451.79715.8820.14130.55110.6554-0.46250.2821-0.3571-2.51490.90050.09331.54180.24180.06060.8903-0.06050.8386-6.334315.2257-10.6092
116.7809-0.0319-1.33927.8041-0.30594.41960.104-0.7826-0.29321.21180.0607-0.49970.78860.1803-0.14451.1271-0.0328-0.2520.5784-0.02250.707912.6124-7.38323.4236
125.5091.6737-1.38438.72780.75858.56680.03190.3467-0.0868-0.14220.18-0.46350.351-0.0751-0.09570.6378-0.046-0.0570.45840.04910.674615.6869-21.68571.6784
137.7901-3.01270.0224.10452.63856.386-0.00830.25710.4529-1.43210.9332-0.5806-2.73360.2602-0.91812.5487-0.05370.13350.9538-0.06571.0305-4.508919.1079-40.792
143.9067-1.78643.00610.8191-1.22353.4134-0.3026-1.8263-0.32693.99371.1352-3.3246-1.4843-0.5926-0.583.1553-0.0778-0.56331.8713-0.28261.3596.18888.7308-20.6658
156.8504-0.05250.55457.5326-5.62486.6442-1.4151-0.31230.26360.68270.2264-1.4687-3.49580.42990.88582.5997-0.2673-0.27830.9499-0.54730.91753.597111.5005-24.1711
167.671-2.18990.75745.45210.69270.2474-1.3352-2.8142.74550.14920.31230.5302-2.0138-1.53140.05313.02010.1484-0.24271.1963-0.49791.215-3.326721.3359-28.9625
179.4399-0.0486-0.29625.05516.03557.32320.4644-0.19321.45833.41940.1837-1.0349-1.76330.0928-0.74462.5420.1102-0.06431.0291-0.1220.9849-2.120914.992-26.4706
188.29923.4129-2.28159.7408-7.33395.5342-1.0022-0.31542.0444-0.43653.5557-2.0799-2.36913.29-3.25661.9952-0.3158-0.1612.0286-0.7831.800111.599123.4978-22.2415
195.08614.88435.1795.82754.48225.4561.0534-0.0047-0.33661.2532-0.7995-3.4599-2.68761.1703-1.1952.1121-0.48150.00741.7871-0.27151.582912.998615.5594-24.0572
203.86241.62570.40492.735-0.12964.9842-0.2094-0.28741.7122-0.43451.9821-1.3242-2.80651.2333-0.85382.6883-0.1657-0.1531.8793-0.68941.20076.178714.4138-24.0098
215.53083.0325.64285.75024.82496.4713.41750.45460.16980.8101-0.4624-1.1791.43731.591-2.17712.0285-0.43450.3812.5874-0.4161.178512.149720.6615-33.8166
224.9291-0.59383.35535.4954-2.97063.4949-0.0804-0.5314-0.5091.6434-0.3258-1.418-1.16034.2772-0.17030.9247-0.1591-0.06832.9537-0.25091.168214.09265.9897-21.4636
238.16-3.98272.23986.1348-4.51963.4167-0.4434-0.07530.84341.6154-0.51890.277-0.08570.04860.67412.7761-0.4676-0.78973.4255-1.31741.228612.576419.7359-12.8668
241.61421.60241.74693.63296.7272.0016-2.608-0.2927-1.88681.16081.0996-1.6128-2.08162.72231.61521.0770.0958-0.1011.32270.34131.62249.028611.3568-1.2166
257.92411.15990.30348.5679-4.59258.816-0.50730.43391.0698-0.250.77020.0528-1.2977-0.1204-0.19591.3918-0.0012-0.02050.9485-0.03910.6222-6.28754.4422-40.6613
266.99683.52415.364.31350.69165.6821-0.9827-0.72170.5384-0.22260.67390.081-1.6961-2.6316-0.84880.97830.29860.00721.93070.23060.8998-18.92580.3882-35.9746
275.03882.4695-4.08376.1646-5.3868.1392-0.1723-0.0683-0.2698-0.531-0.0607-1.8311-0.2513-0.7824-0.12021.551-0.2061-0.01581.3618-0.02730.7261-6.92793.9097-52.1344
286.12063.3213-3.53674.9047-3.41054.9701-0.74380.8634-1.2328-0.90220.3462-0.44380.6799-0.37650.4651.0441-0.04170.21260.9747-0.22040.8765-12.1706-17.0657-29.6497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 102 )
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 110 )
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 126 )
9X-RAY DIFFRACTION9chain 'C' and (resid 100 through 111 )
10X-RAY DIFFRACTION10chain 'C' and (resid 112 through 121 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 92 )
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 240 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 32 )
14X-RAY DIFFRACTION14chain 'D' and (resid 33 through 39 )
15X-RAY DIFFRACTION15chain 'D' and (resid 40 through 59 )
16X-RAY DIFFRACTION16chain 'D' and (resid 60 through 70 )
17X-RAY DIFFRACTION17chain 'D' and (resid 71 through 83 )
18X-RAY DIFFRACTION18chain 'D' and (resid 84 through 89 )
19X-RAY DIFFRACTION19chain 'D' and (resid 90 through 97 )
20X-RAY DIFFRACTION20chain 'D' and (resid 98 through 110 )
21X-RAY DIFFRACTION21chain 'D' and (resid 111 through 122 )
22X-RAY DIFFRACTION22chain 'F' and (resid 101 through 110 )
23X-RAY DIFFRACTION23chain 'F' and (resid 111 through 115 )
24X-RAY DIFFRACTION24chain 'F' and (resid 116 through 121 )
25X-RAY DIFFRACTION25chain 'E' and (resid 0 through 47 )
26X-RAY DIFFRACTION26chain 'E' and (resid 48 through 60 )
27X-RAY DIFFRACTION27chain 'E' and (resid 61 through 85 )
28X-RAY DIFFRACTION28chain 'E' and (resid 86 through 241 )

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