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- PDB-4b6h: Structure of hDcp1a in complex with proline rich sequence of PNRC2 -

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Basic information

Entry
Database: PDB / ID: 4b6h
TitleStructure of hDcp1a in complex with proline rich sequence of PNRC2
Components
  • MRNA-DECAPPING ENZYME 1A
  • PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / DECAPPING
Function / homology
Function and homology information


mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / protein localization to cytoplasmic stress granule / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / protein localization to cytoplasmic stress granule / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / kinesin binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / P-body / enzyme activator activity / cytoplasmic ribonucleoprotein granule / mRNA binding / dendrite / DNA-templated transcription / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proline-rich nuclear receptor coactivator 1/2 / mRNA-decapping enzyme, C-terminal / mRNA-decapping enzyme C-terminus / : / Proline-rich nuclear receptor coactivator motif / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...Proline-rich nuclear receptor coactivator 1/2 / mRNA-decapping enzyme, C-terminal / mRNA-decapping enzyme C-terminus / : / Proline-rich nuclear receptor coactivator motif / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
mRNA-decapping enzyme 1A / Proline-rich nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLai, T. / Song, H.
CitationJournal: Structure / Year: 2012
Title: Structural Basis of the Pnrc2-Mediated Link between Mrna Surveillance and Decapping.
Authors: Lai, T. / Cho, H. / Liu, Z. / Bowler, M.W. / Piao, S. / Parker, R. / Kim, Y.K. / Song, H.
History
DepositionAug 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA-DECAPPING ENZYME 1A
B: MRNA-DECAPPING ENZYME 1A
C: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2
D: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2


Theoretical massNumber of molelcules
Total (without water)61,2374
Polymers61,2374
Non-polymers00
Water1,18966
1
A: MRNA-DECAPPING ENZYME 1A
C: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2


Theoretical massNumber of molelcules
Total (without water)30,6182
Polymers30,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10.5 kcal/mol
Surface area8130 Å2
MethodPISA
2
B: MRNA-DECAPPING ENZYME 1A
D: PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2


Theoretical massNumber of molelcules
Total (without water)30,6182
Polymers30,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-11.2 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.091, 97.639, 109.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 27:43 OR RESSEQ 48:75 OR RESSEQ 81:130 )
211CHAIN B AND (RESSEQ 27:43 OR RESSEQ 48:75 OR RESSEQ 81:130 )
112CHAIN C AND (RESSEQ 170:180 )
212CHAIN D AND (RESSEQ 170:180 )

NCS ensembles :
ID
1
2

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Components

#1: Protein MRNA-DECAPPING ENZYME 1A / HDCP1A / SMAD4-INTERACTING TRANSCRIPTIONAL CO-ACTIVATOR / TRANSCRIPTION FACTOR SMIF


Mass: 15492.594 Da / Num. of mol.: 2 / Fragment: EVH1 DOMAIN, RESIDUES 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: Q9NPI6, Hydrolases
#2: Protein PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2 / PNRC2


Mass: 15125.746 Da / Num. of mol.: 2 / Fragment: PROLINE RICH SEQUENCE, RESIDUES 1-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: Q9NPJ4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.18 Å3/Da / Density % sol: 61.4 % / Description: NONE
Crystal growDetails: 27% PEG3350, 0.15M AMMONIUM ACETATE, 0.1M BIS TRIS PH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→72 Å / Num. obs: 12614 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 2.6→2.6 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→72.931 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 1262 10 %
Rwork0.2335 --
obs0.2388 12614 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.522 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3046 Å20 Å20 Å2
2---6.005 Å20 Å2
3---4.7004 Å2
Refinement stepCycle: LAST / Resolution: 2.6→72.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 66 2152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082137
X-RAY DIFFRACTIONf_angle_d1.2392902
X-RAY DIFFRACTIONf_dihedral_angle_d17.725771
X-RAY DIFFRACTIONf_chiral_restr0.082319
X-RAY DIFFRACTIONf_plane_restr0.004366
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A782X-RAY DIFFRACTIONPOSITIONAL
12B782X-RAY DIFFRACTIONPOSITIONAL0.241
21C89X-RAY DIFFRACTIONPOSITIONAL
22D89X-RAY DIFFRACTIONPOSITIONAL0.196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.70420.41581410.31741267X-RAY DIFFRACTION100
2.7042-2.82720.3541420.29721275X-RAY DIFFRACTION99
2.8272-2.97630.34591390.28691258X-RAY DIFFRACTION100
2.9763-3.16280.33641410.27291275X-RAY DIFFRACTION100
3.1628-3.4070.31691400.25281255X-RAY DIFFRACTION99
3.407-3.74980.2641430.23021279X-RAY DIFFRACTION99
3.7498-4.29240.27421400.18761264X-RAY DIFFRACTION98
4.2924-5.40770.19571400.17051264X-RAY DIFFRACTION97
5.4077-72.95920.30181360.24561215X-RAY DIFFRACTION88
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)
11.8331-0.27963.96972.9482-0.54518.4976-0.18560.2046-1.0936-0.7506-0.32470.0442-0.2097-1.45430.74350.43960.0793-0.04450.1384-0.1040.3876-4.5729-43.517-0.7444
28.4808-1.3124-3.66410.41380.52131.7932-0.0049-0.2919-2.1642-0.0077-0.4915-0.0536-0.29690.52420.33470.5104-0.0628-0.03620.31980.07170.591-11.792-44.661714.8732
32.863-0.7142.51893.82090.48343.69750.3341-0.24440.9582-0.3044-0.3087-1.03680.2461-0.3593-0.11820.2456-0.00560.0210.3484-0.19560.59432.817-25.685119.8896
43.3990.4573-1.32984.0965-0.35917.64430.1052-0.28970.0423-0.05340.27170.14010.4170.4243-0.41750.2563-0.0399-0.03340.17420.04950.2409-11.0937-36.562815.663
54.4977-1.16970.95422.74621.30761.4845-0.25590.4781-0.86611.44670.279-0.31371.0955-0.24450.00540.48040.0058-0.03670.4666-0.0430.2868-2.3556-36.785619.2284
62.3347-1.54261.28552.7841-2.10771.94850.037-0.73621.1589-0.6575-1.3770.2714-0.11730.1674-0.64650.4441-0.22920.13460.5069-0.3964-0.0032-10.3542-21.508819.1481
73.176-0.9856-0.01684.04192.08813.25790.6601-0.75240.65250.4080.5276-0.9835-0.7840.4223-0.90020.1891-0.09140.08420.3301-0.10860.3702-3.3916-24.489318.8981
87.016-3.6768-2.67624.55360.19382.88380.22360.66870.4593-0.8712-0.2854-0.5975-0.3179-0.7086-0.10490.27250.01-0.08360.3646-0.0540.2239-13.2603-25.688411.0533
95.2427-4.07980.52854.7907-3.0641.99130.31090.44061.1219-0.7401-0.6889-1.27582.3816-1.37990.52030.1557-0.02420.2040.5906-0.12040.5959-10.0155-3.649425.5909
104.37270.2196-4.15793.9767-0.6545.64880.50673.2345-0.0132-0.6046-0.1657-1.10310.3680.418-0.08550.61520.3574-0.06080.71130.01550.6186-29.1931-6.9715.0311
119.7894-6.84010.31139.7694.61836.86321.06060.99661.4577-4.4992-1.88290.6526-1.6734-0.53691.28291.02340.4202-0.36050.9319-0.19560.1175-29.8843-3.944612.7605
125.3854-3.8971-3.6588.30276.41595.06390.5856-0.24131.7442-0.08341.3002-2.7089-0.18540.6553-1.93840.4415-0.12150.12840.5213-0.23330.7972-14.3517-3.594628.9943
132.10160.2499-0.89067.75561.30131.0231.11950.28773.9286-2.454-0.74391.03260.8276-0.4149-0.41970.7375-0.01260.21930.46120.1911.4414-18.60382.476116.0705
145.18822.38143.94026.31267.2168.64441.28610.7356-0.20691.3676-0.4532-1.08531.7885-1.54650.71370.35620.11240.14160.4084-0.10210.3883-24.9094-9.643127.1241
158.06180.6079-1.98123.55720.87493.6004-0.0521.46021.2278-0.1544-0.6962-0.3561-0.5206-1.25510.67220.52490.2994-0.01360.8619-0.02810.4572-26.3347-9.711620.0063
160.51261.53590.53773.83771.51150.52980.42570.2183-0.31720.6539-0.7185-0.02420.4091-0.16690.01850.5381-0.04440.14330.5998-0.11290.3184-17.0855-15.840724.379
175.6818-0.2202-1.93831.30631.81654.20180.699-0.27452.3812-0.52630.5591-0.42130.05470.3144-1.16950.361-0.00020.07750.3788-0.11160.79890.1781-17.29621.4707
186.38963.85124.66979.57998.34887.730.7629-1.1785-0.07151.7965-2.09411.27882.8557-1.4840.02380.42340.1707-0.0380.5376-0.11690.2377-34.2789-13.828818.8035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:15)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 16:31)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 32:54)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 55:74)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 75:87)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 88:96)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 97:114)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 115:134)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 24:35)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 36:46)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 47:55)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 56:71)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 72:81)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 82:96)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 97:115)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 116:130)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 167:180)
18X-RAY DIFFRACTION18(CHAIN D AND RESID 167:180)

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