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- PDB-1xmm: Structure of human Dcps bound to m7GDP -

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Basic information

Entry
Database: PDB / ID: 1xmm
TitleStructure of human Dcps bound to m7GDP
Componentsheat shock-like protein 1
KeywordsCHAPERONE / scavenger decapping enzyme bound m7GDP
Function / homology
Function and homology information


mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / 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 ...mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / 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 / HIT family, subunit A / HIT-like superfamily / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / : / m7GpppX diphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, N. / Song, H.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping.
Authors: Chen, N. / Walsh, M.A. / Liu, Y. / Parker, R. / Song, H.
History
DepositionOct 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: heat shock-like protein 1
A: heat shock-like protein 1
C: heat shock-like protein 1
D: heat shock-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,35012
Polymers156,2974
Non-polymers2,0538
Water7,548419
1
B: heat shock-like protein 1
A: heat shock-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1756
Polymers78,1482
Non-polymers1,0264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-65 kcal/mol
Surface area24940 Å2
MethodPISA
2
C: heat shock-like protein 1
D: heat shock-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1756
Polymers78,1482
Non-polymers1,0264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-67 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.928, 105.140, 138.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsFunctional unit is dimer. There are two functional units in the assymmetric unit

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Components

#1: Protein
heat shock-like protein 1 / Dcps


Mass: 39074.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 30138167, UniProt: Q96C86*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-G7M / N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 378.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O8P
#4: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.4 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG3350, KH2PO4, NaCl, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9997 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.5→32.6 Å / Num. all: 51115 / Num. obs: 51097 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.887 / SU B: 9.05 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.611 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26695 2509 4.9 %RANDOM
Rwork0.21353 ---
all0.216 48479 --
obs0.21615 48479 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.474 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---0.05 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 128 419 10108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219920
X-RAY DIFFRACTIONr_bond_other_d0.0020.029027
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.97713479
X-RAY DIFFRACTIONr_angle_other_deg0.781320961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79751145
X-RAY DIFFRACTIONr_chiral_restr0.0740.21484
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210845
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022037
X-RAY DIFFRACTIONr_nbd_refined0.1940.21973
X-RAY DIFFRACTIONr_nbd_other0.2180.210519
X-RAY DIFFRACTIONr_nbtor_other0.0820.25997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2390
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.29
X-RAY DIFFRACTIONr_mcbond_it0.4191.55793
X-RAY DIFFRACTIONr_mcangle_it0.80329394
X-RAY DIFFRACTIONr_scbond_it1.04534127
X-RAY DIFFRACTIONr_scangle_it1.8514.54085
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 160
Rwork0.246 3082
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)
11.06290.1070.15390.8194-0.02790.2404-0.03610.03720.0158-0.0505-0.0097-0.0173-0.0270.01440.04580.1160.005-0.00060.1044-0.00440.108334.703240.51824.3861
21.99-0.05710.22480.5725-0.36920.396-0.0040.0088-0.11260.00340.07440.0030.0364-0.01-0.07030.0998-0.0015-0.00250.09770.01160.103846.175523.593241.6582
31.87680.2954-0.19790.4491-0.26130.32570.0035-0.02870.13980.05370.07860.0128-0.02710.0032-0.0820.0975-0.0068-0.00020.12330.00710.101196.601432.719626.7681
40.9221-0.0968-0.26290.82160.09580.465-0.035-0.0732-0.00970.0274-0.0110.00180.03040.01820.0460.1104-0.003-0.01250.09860.01210.115485.258416.208144.3794
51.0755-0.1479-0.09381.9606-0.38871.1229-0.07650.0218-0.2243-0.08510.0616-0.07320.19720.0470.01480.1417-0.00670.06290.1263-0.06320.083741.193718.96467.0344
60.85480.40540.04632.7528-0.31861.1968-0.1235-0.04490.24060.00630.08080.0732-0.17820.14210.04270.1387-0.0416-0.08780.1275-0.02570.079191.910338.155460.6742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB146 - 336151 - 341
2X-RAY DIFFRACTION2BA146 - 336151 - 341
3X-RAY DIFFRACTION3CC146 - 336151 - 341
4X-RAY DIFFRACTION4DD146 - 336151 - 341
5X-RAY DIFFRACTION5AB40 - 14545 - 150
6X-RAY DIFFRACTION5BA40 - 14545 - 150
7X-RAY DIFFRACTION6CC39 - 14544 - 150
8X-RAY DIFFRACTION6DD40 - 14545 - 150

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