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- PDB-5kq4: Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapien... -

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Basic information

Entry
Database: PDB / ID: 5kq4
TitleCrystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2 and synthetic cap analog
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 / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-independent decapping of nuclear-transcribed mRNA / 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 ...mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-independent decapping of nuclear-transcribed mRNA / 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 / nuclear-transcribed mRNA catabolic process / 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 / magnesium ion binding / Golgi apparatus / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proline-rich nuclear receptor coactivator 1/2 / : / Proline-rich nuclear receptor coactivator motif / Dcp2, box A domain / 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 ...Proline-rich nuclear receptor coactivator 1/2 / : / Proline-rich nuclear receptor coactivator motif / Dcp2, box A domain / 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 / 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 / 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: 2.56 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 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 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
D: mRNA-decapping enzyme subunit 1
F: Proline-rich nuclear receptor coactivator 2
E: mRNA decapping complex subunit 2
A: mRNA-decapping enzyme subunit 1
C: Proline-rich nuclear receptor coactivator 2
B: mRNA decapping complex subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1548
Polymers95,2936
Non-polymers1,8612
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-51 kcal/mol
Surface area38680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.067, 120.752, 91.849
Angle α, β, γ (deg.)90.00, 97.90, 90.00
Int Tables number4
Space group name H-MP1211
DetailsGel filtration, SDS PAGE performed. Chains (A,B,C) and (D,E,F) form a dimer in solution with one another.

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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
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
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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.48 Å3/Da / Density % sol: 50.45 % / Description: Plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 150 mM trilithium citrate, 13% PEG 3350, 0.05% mellitic acid, ~4 mM ZD3 soak

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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: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 29862 / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.115 / Net I/av σ(I): 25.586 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.55-2.613.90.940.626199.9
2.61-2.6740.9530.4321100
2.67-2.7340.9360.7431100
2.73-2.8140.4640.8611100
2.81-2.894.10.3680.9071100
2.89-2.9840.2820.9341100
2.98-3.094.10.2240.9631100
3.09-3.2140.1750.9741100
3.21-3.364.10.130.9861100
3.36-3.5440.2530.8341100
3.54-3.7640.1820.897199.9
3.76-4.0540.1670.921100
4.05-4.4540.0730.9921100
4.45-5.140.070.991100
5.1-6.423.90.0580.9951100
6.42-5040.0420.998199.4

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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: 2.56→45.489 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1460 4.91 %
Rwork0.2065 --
obs0.2087 29761 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→45.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6347 0 114 27 6488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036641
X-RAY DIFFRACTIONf_angle_d0.6559021
X-RAY DIFFRACTIONf_dihedral_angle_d20.1823933
X-RAY DIFFRACTIONf_chiral_restr0.046965
X-RAY DIFFRACTIONf_plane_restr0.0041135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.65150.38041540.36472655X-RAY DIFFRACTION95
2.6515-2.75770.4211450.34012799X-RAY DIFFRACTION99
2.7577-2.88310.29031590.27092857X-RAY DIFFRACTION100
2.8831-3.03510.28041320.24742848X-RAY DIFFRACTION100
3.0351-3.22520.28521390.24722850X-RAY DIFFRACTION100
3.2252-3.47420.26521390.24822824X-RAY DIFFRACTION100
3.4742-3.82360.27091530.20682865X-RAY DIFFRACTION100
3.8236-4.37650.21771520.1882845X-RAY DIFFRACTION100
4.3765-5.51240.19511440.15882853X-RAY DIFFRACTION100
5.5124-45.49570.23821430.17492905X-RAY DIFFRACTION100
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)
18.6143-1.28593.50317.41360.4592.5894-0.4367-0.94890.39690.96270.3844-0.4293-0.0917-0.2750.02610.48380.0351-0.10810.553-0.14250.541712.03912.262621.7916
29.3743-0.49884.6124.0524-0.346.23930.65010.7083-0.8428-0.40210.07580.47930.18050.3303-0.82950.4590.0069-0.06680.3186-0.04730.52290.52098.57524.2513
35.6394-2.36392.48391.20510.39598.011-0.1526-0.27950.6668-0.18410.1435-0.7648-0.65460.29130.1250.3405-0.06910.01380.323-0.04860.54198.766513.77318.8404
48.7122-6.0582.02697.02920.99835.6913-0.22450.0172-0.3785-0.74910.09120.4132-0.38390.08890.07210.4768-0.0148-0.13450.3897-0.00440.4633-3.632716.96814.2561
58.8998-2.6362-0.6495.0753-0.55336.8572-0.096-1.3930.25320.6724-0.2080.0136-0.774-0.47210.26090.40720.0168-0.10820.5121-0.05130.5873-3.787315.261614.8076
64.6441-2.65620.96534.855-1.25710.57121.5547-1.2146-1.5772-0.3530.49292.36231.509-0.0443-1.49310.64870.0277-0.1020.52480.13510.9395-8.33580.60855.8992
74.8279-3.37473.49125.6177-4.97294.48680.35580.2581-0.0776-1.916-0.41481.6942-0.595-0.16120.06450.66870.0553-0.10.4646-0.03150.4153-9.481916.0168-1.2925
82.3174-1.475-0.58933.27122.72662.52850.4031.956-1.5566-1.0702-0.64350.4146-2.0853-1.91450.69010.7941-0.01060.05571.4198-0.46861.0477-6.320116.2201-16.6032
93.7204-0.17550.85777.524-0.31667.6849-0.0046-0.5854-0.18540.7477-0.07690.1123-0.0209-0.22690.04350.3958-0.0312-0.09480.4075-0.01590.444514.7604-3.93120.4437
103.01330.3942-0.63075.39192.07797.21920.0618-0.0995-0.0234-0.0562-0.05490.220.6656-0.12610.04150.4144-0.01720.0160.29980.03030.391511.0803-22.386.0857
115.5749-0.0691-1.39357.52110.9488.8531-0.09560.06870.1124-0.59270.1936-0.4303-0.01320.5771-0.12040.4920.01010.03120.40160.04730.407120.3395-18.1152-2.0666
129.07760.5657-0.89315.62790.16656.64930.01391.0268-0.127-2.1846-0.1984-0.8691-2.6152-0.39840.54821.6604-0.02880.09830.711-0.17220.8999-7.151220.1494-47.0478
136.79972.5764-1.90865.2336-1.92664.40530.0325-1.10762.3829-0.1184-0.28911.8064-1.729-0.25240.30531.10630.26170.07740.8197-0.28621.0383-9.419426.0642-35.963
143.3498-1.56843.35215.0453-3.0223.8320.65250.0345-0.1459-0.4091-0.0603-0.6773-0.57161.6127-0.72431.0266-0.17150.04130.9098-0.14960.86723.388413.9248-29.96
155.4655-0.55182.58012.1893-1.63428.51040.2353-0.66350.02751.01740.2611-0.1537-0.5936-0.1902-0.6740.9955-0.0455-0.01370.7464-0.13520.71991.320613.7224-26.1885
169.31032.66933.00175.08281.12747.5038-0.4643-0.33941.3420.35770.1320.5331-0.76690.26240.43090.7524-0.06410.00440.716-0.14740.6657-5.765418.4619-31.6205
178.0272.6162.60564.33551.83887.1986-0.7701-0.02921.8257-0.94190.4736-0.782-1.7629-0.3820.39611.0154-0.0179-0.08480.5979-0.07560.9872-1.2124.7435-26.4899
182.31830.5753.39934.0890.48146.47080.18-0.21810.52610.73650.5661-1.4257-0.37490.4273-0.46560.9367-0.10940.01911.1288-0.50221.38537.432320.5651-23.3855
198.1041-3.98962.20217.9077-0.9995.75150.26611.18130.7752-1.40980.0274-2.4616-0.74131.2737-0.28460.9393-0.28770.40491.226-0.36471.34249.177119.8094-33.9111
200.99360.32150.23133.85691.75323.08540.1960.3066-0.73951.00971.1487-0.56580.40811.9593-1.38160.7780.34430.00231.597-0.17431.30919.12953.6821-28.5294
217.06920.3072.27884.779-1.36232.80320.80160.1593-1.5529-0.1743-0.32881.0395-1.4111.10380.24410.8949-0.0099-0.18441.2806-0.21461.180211.046915.9191-11.4606
226.0148-0.1152-1.49677.60153.46168.68360.0370.5049-0.019-0.4938-0.08570.1585-0.2927-0.20660.03220.59230.039-0.06890.55-0.02820.336-10.01763.7367-46.2735
235.63420.7404-2.10786.5785-2.60478.3429-0.1277-0.1182-0.2562-0.4755-0.0661-0.2241.00260.21110.1890.8080.01580.08260.6085-0.04190.4874-16.7799-19.2558-32.0101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'D' and (resid 33 through 59 )
3X-RAY DIFFRACTION3chain 'D' and (resid 60 through 83 )
4X-RAY DIFFRACTION4chain 'D' and (resid 84 through 102 )
5X-RAY DIFFRACTION5chain 'D' and (resid 103 through 126 )
6X-RAY DIFFRACTION6chain 'F' and (resid 100 through 106 )
7X-RAY DIFFRACTION7chain 'F' and (resid 107 through 114 )
8X-RAY DIFFRACTION8chain 'F' and (resid 115 through 121 )
9X-RAY DIFFRACTION9chain 'E' and (resid 0 through 82 )
10X-RAY DIFFRACTION10chain 'E' and (resid 83 through 176 )
11X-RAY DIFFRACTION11chain 'E' and (resid 177 through 240 )
12X-RAY DIFFRACTION12chain 'A' and (resid 1 through 19 )
13X-RAY DIFFRACTION13chain 'A' and (resid 20 through 26 )
14X-RAY DIFFRACTION14chain 'A' and (resid 27 through 39 )
15X-RAY DIFFRACTION15chain 'A' and (resid 40 through 59 )
16X-RAY DIFFRACTION16chain 'A' and (resid 60 through 76 )
17X-RAY DIFFRACTION17chain 'A' and (resid 77 through 83 )
18X-RAY DIFFRACTION18chain 'A' and (resid 84 through 102 )
19X-RAY DIFFRACTION19chain 'A' and (resid 103 through 124 )
20X-RAY DIFFRACTION20chain 'C' and (resid 99 through 106 )
21X-RAY DIFFRACTION21chain 'C' and (resid 107 through 121 )
22X-RAY DIFFRACTION22chain 'B' and (resid -2 through 95 )
23X-RAY DIFFRACTION23chain 'B' and (resid 96 through 239 )

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