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- PDB-6trq: S.c. Scavenger Decapping Enzyme DcpS in complex with the capped R... -

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Basic information

Entry
Database: PDB / ID: 6trq
TitleS.c. Scavenger Decapping Enzyme DcpS in complex with the capped RNA dinucleotide m7G-GU
Componentsm7GpppX diphosphatase
KeywordsHYDROLASE / mRNA decapping / mRNA degradation / decapping
Function / homology
Function and homology information


exoribonuclease activator activity / m7G(5')pppN diphosphatase complex / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / RNA 7-methylguanosine cap binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...exoribonuclease activator activity / m7G(5')pppN diphosphatase complex / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / RNA 7-methylguanosine cap binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / response to osmotic stress / cellular response to starvation / response to nutrient / P-body / response to heat / response to oxidative stress / protein heterodimerization activity / perinuclear region of cytoplasm / protein homodimerization activity / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like superfamily
Similarity search - Domain/homology
L-GUANOSINE-5'-MONOPHOSPHATE / PHOSPHONATE / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / URIDINE-5'-MONOPHOSPHATE / m7GpppX diphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.944 Å
AuthorsFuchs, A.-L. / Neu, A. / Sprangers, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council616052 Germany
German Research FoundationSFB 960/2, B12 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular basis of the selective processing of short mRNA substrates by the DcpS mRNA decapping enzyme.
Authors: Fuchs, A.L. / Wurm, J.P. / Neu, A. / Sprangers, R.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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
Revision 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Mar 6, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: m7GpppX diphosphatase
B: m7GpppX diphosphatase
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,48714
Polymers160,8444
Non-polymers2,64310
Water362
1
A: m7GpppX diphosphatase
B: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6476
Polymers80,4222
Non-polymers1,2264
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-91 kcal/mol
Surface area27580 Å2
MethodPISA
2
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8408
Polymers80,4222
Non-polymers1,4186
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-125 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.761, 104.103, 189.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 54 or resid 67...
21(chain B and (resid 7 through 54 or resid 67...
31(chain C and (resid 7 through 54 or resid 67...
41(chain D and (resid 7 through 182 or (resid 185...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU(chain A and (resid 7 through 54 or resid 67...AA7 - 542 - 49
12PROPROCYSCYS(chain A and (resid 7 through 54 or resid 67...AA67 - 15462 - 149
13LYSLYSMETMET(chain A and (resid 7 through 54 or resid 67...AA160 - 195155 - 190
14ASNASNLYSLYS(chain A and (resid 7 through 54 or resid 67...AA201 - 344196 - 339
21METMETGLUGLU(chain B and (resid 7 through 54 or resid 67...BB7 - 542 - 49
22PROPROGLUGLU(chain B and (resid 7 through 54 or resid 67...BB67 - 18262 - 177
23GLYGLYLYSLYS(chain B and (resid 7 through 54 or resid 67...BB6 - 3441 - 339
24GLYGLYLYSLYS(chain B and (resid 7 through 54 or resid 67...BB6 - 3441 - 339
25GLYGLYLYSLYS(chain B and (resid 7 through 54 or resid 67...BB6 - 3441 - 339
26GLYGLYLYSLYS(chain B and (resid 7 through 54 or resid 67...BB6 - 3441 - 339
27GLYGLYLYSLYS(chain B and (resid 7 through 54 or resid 67...BB6 - 3441 - 339
28GLYGLYLYSLYS(chain B and (resid 7 through 54 or resid 67...BB6 - 3441 - 339
29GLYGLYLYSLYS(chain B and (resid 7 through 54 or resid 67...BB6 - 3441 - 339
31METMETGLUGLU(chain C and (resid 7 through 54 or resid 67...CC7 - 542 - 49
32PROPROCYSCYS(chain C and (resid 7 through 54 or resid 67...CC67 - 15462 - 149
33LYSLYSGLUGLU(chain C and (resid 7 through 54 or resid 67...CC160 - 182155 - 177
34LYSLYSLYSLYS(chain C and (resid 7 through 54 or resid 67...CC185180
35GLYGLYILEILE(chain C and (resid 7 through 54 or resid 67...CC6 - 3451 - 340
36GLYGLYILEILE(chain C and (resid 7 through 54 or resid 67...CC6 - 3451 - 340
37GLYGLYILEILE(chain C and (resid 7 through 54 or resid 67...CC6 - 3451 - 340
38GLYGLYILEILE(chain C and (resid 7 through 54 or resid 67...CC6 - 3451 - 340
39GLYGLYILEILE(chain C and (resid 7 through 54 or resid 67...CC6 - 3451 - 340
41METMETGLUGLU(chain D and (resid 7 through 182 or (resid 185...DD7 - 1822 - 177
42LYSLYSLYSLYS(chain D and (resid 7 through 182 or (resid 185...DD185180
43GLYGLYLYSLYS(chain D and (resid 7 through 182 or (resid 185...DD6 - 3441 - 339
44GLYGLYLYSLYS(chain D and (resid 7 through 182 or (resid 185...DD6 - 3441 - 339
45GLYGLYLYSLYS(chain D and (resid 7 through 182 or (resid 185...DD6 - 3441 - 339
46GLYGLYLYSLYS(chain D and (resid 7 through 182 or (resid 185...DD6 - 3441 - 339

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
m7GpppX diphosphatase / / DCS-1 / Hint-related 7meGMP-directed hydrolase 1 / Protein Dcs1p / Scavenger mRNA-decapping enzyme DcpS


Mass: 40210.883 Da / Num. of mol.: 4 / Mutation: H268N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: DCS1, YLR270W / Production host: Escherichia coli (E. coli)
References: UniProt: Q06151, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase

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Non-polymers , 6 types, 12 molecules

#2: Chemical ChemComp-2PO / PHOSPHONATE / Phosphonate


Mass: 79.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO3P
#3: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Chemical ChemComp-0G / L-GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Type: L-RNA linking / Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM NaCl 100 mM Hepes pH 7.5 1.6 M NH4SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.94→47.306 Å / Num. obs: 70791 / % possible obs: 99.7 % / Redundancy: 13.338 % / Biso Wilson estimate: 58.022 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.312 / Rrim(I) all: 0.325 / Χ2: 0.884 / Net I/σ(I): 9.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.94-3.0213.6352.471.1936147274526510.6342.56596.6
3.02-3.113.8912.0071.5236852265526530.7562.08399.9
3.1-3.1913.7761.6961.8535570258325820.851.761100
3.19-3.2913.5131.4312.233917251125100.8771.486100
3.29-3.413.2431.0822.932484245324530.9231.125100
3.4-3.5212.4640.853.4829651238023790.940.887100
3.52-3.6513.2290.6594.6430282229122890.9660.68699.9
3.65-3.813.9070.4956.2930511219521940.9820.514100
3.8-3.9713.7990.4057.429350212821270.9850.42100
3.97-4.1613.6190.3039.2827851204520450.9890.315100
4.16-4.3913.4110.21712.0125937193419340.9940.225100
4.39-4.6612.5180.15614.4822796182118210.9980.162100
4.66-4.9813.4340.13916.623361173917390.9980.145100
4.98-5.3813.8520.16615.1122412161816180.9970.173100
5.38-5.8913.4730.17814.3220277150515050.9940.185100
5.89-6.5812.8050.16114.9417312135213520.9960.168100
6.58-7.612.3720.12318.2215118122212220.9970.128100
7.6-9.3113.30.07329.9613898104510450.9990.076100
9.31-13.1711.9390.04839.2599338328320.9990.05100
13.17-47.30611.7140.04836.9257755094930.9990.0596.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.91 Å47.31 Å
Translation7.91 Å47.31 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bv3

5bv3


Resolution: 2.944→47.306 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.94
RfactorNum. reflection% reflection
Rfree0.2631 3547 5.02 %
Rwork0.2043 --
obs0.2072 67044 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 189.21 Å2 / Biso mean: 82.52 Å2 / Biso min: 31.74 Å2
Refinement stepCycle: final / Resolution: 2.944→47.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10753 0 236 2 10991
Biso mean--95.7 37.8 -
Num. residues----1309
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6258X-RAY DIFFRACTION14.782TORSIONAL
12B6258X-RAY DIFFRACTION14.782TORSIONAL
13C6258X-RAY DIFFRACTION14.782TORSIONAL
14D6258X-RAY DIFFRACTION14.782TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9442-2.98450.36261290.3578249993
2.9845-3.02720.40721450.362735100
3.0272-3.07230.37511380.35352655100
3.0723-3.12030.36931440.32772672100
3.1203-3.17150.36451490.3452706100
3.1715-3.22620.4261390.33142652100
3.2262-3.28480.38631420.3122696100
3.2848-3.3480.3241430.28482713100
3.348-3.41630.32541420.26952671100
3.4163-3.49060.34951410.26672718100
3.4906-3.57170.32161440.25542665100
3.5717-3.6610.3091380.24442715100
3.661-3.760.26891420.22252657100
3.76-3.87060.34121430.20582697100
3.8706-3.99540.26521430.18292717100
3.9954-4.13810.22081390.17172668100
4.1381-4.30370.24991380.16562690100
4.3037-4.49940.20561410.14712698100
4.4994-4.73650.20071460.14022709100
4.7365-5.03290.18661420.13862644100
5.0329-5.4210.17091450.15132718100
5.421-5.96560.23921420.16112682100
5.9656-6.82660.25961440.18322707100
6.8266-8.59240.23691390.16312686100
8.5924-47.3060.21611490.178267499
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)
12.2293-0.4746-0.3260.77640.36542.1682-0.15580.31980.0159-0.43240.0230.07510.2884-0.52480.11231.185-0.1015-0.03930.50570.00290.400930.4907-12.726832.3783
20.80020.17210.51511.38470.16864.3117-0.06510.0940.0553-0.22770.0743-0.0866-0.06720.233-0.01220.7888-0.00430.04550.3250.02610.375841.972610.835431.9232
31.3360.1864-0.11550.9114-0.5131.7936-0.063-0.2543-0.2278-0.35920.10660.06550.4978-0.5544-0.03610.9631-0.1192-0.03780.59380.01790.398622.771-11.319636.0746
41.59610.41390.21781.86961.0926.65380.09680.09150.0615-0.0897-0.13030.0867-0.3495-0.64670.02940.67230.07670.01680.38410.00320.410723.299219.475245.293
50.63120.91310.24941.4107-0.11022.415-0.0122-0.410.27361.2950.2768-0.5160.43270.3021-0.14890.74610.1092-0.07780.5839-0.0360.390635.6367-4.523586.8729
60.666-0.2670.00241.67190.52641.83940.0204-0.0032-0.12420.5614-0.03110.06271.055-0.13930.01341.021-0.01870.02360.4911-0.02720.334331.093-11.198177.6853
78.2321-0.0218-4.49191.66372.80138.087-0.3498-0.6769-0.6010.2015-0.26260.15511.39560.35040.55691.42430.10250.01010.545-0.00460.463326.263-24.919198.5812
81.5102-0.9845-0.26811.13980.29973.2517-0.16350.0545-0.24880.4060.04330.18071.157-0.7050.12381.2631-0.20880.15970.6204-0.03770.481216.6247-20.128483.0076
91.9212-1.69160.3185.2036-1.20723.5721-0.2483-0.09710.27090.61790.1326-0.4025-0.37470.09030.10840.6953-0.0240.01640.4353-0.03010.288734.56545.577580.367
100.63640.23150.35062.00130.35515.3063-0.25690.25990.1327-0.22480.02490.21410.3655-1.55450.26020.6417-0.1917-0.03061.0349-0.05440.47464.4994-7.629171.3834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 127 )A7 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 346 )A128 - 346
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 138 )B6 - 138
4X-RAY DIFFRACTION4chain 'B' and (resid 139 through 344 )B139 - 344
5X-RAY DIFFRACTION5chain 'C' and (resid 7 through 81 )C7 - 81
6X-RAY DIFFRACTION6chain 'C' and (resid 82 through 153 )C82 - 153
7X-RAY DIFFRACTION7chain 'C' and (resid 154 through 193 )C154 - 193
8X-RAY DIFFRACTION8chain 'C' and (resid 194 through 345 )C194 - 345
9X-RAY DIFFRACTION9chain 'D' and (resid 6 through 127 )D6 - 127
10X-RAY DIFFRACTION10chain 'D' and (resid 128 through 344 )D128 - 344

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