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- PDB-3d3k: Crystal structure of human Edc3p -

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Basic information

Entry
Database: PDB / ID: 3d3k
TitleCrystal structure of human Edc3p
ComponentsEnhancer of mRNA-decapping protein 3
KeywordsPROTEIN BINDING / hEdc3 / Phosphoprotein
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / P-body assembly / P-body / cytoplasmic ribonucleoprotein granule / mRNA binding / identical protein binding / membrane / cytosol
Similarity search - Function
Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF ...Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / : / Sm domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLing, S.H.M.
CitationJournal: Mol.Cell.Biol. / Year: 2008
Title: Crystal structure of human Edc3 and its functional implications
Authors: Ling, S.H.M. / Decker, C.J. / Walsh, M.A. / She, M. / Parker, R. / Song, H.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enhancer of mRNA-decapping protein 3
B: Enhancer of mRNA-decapping protein 3
C: Enhancer of mRNA-decapping protein 3
D: Enhancer of mRNA-decapping protein 3


Theoretical massNumber of molelcules
Total (without water)114,3494
Polymers114,3494
Non-polymers00
Water6,269348
1
A: Enhancer of mRNA-decapping protein 3
B: Enhancer of mRNA-decapping protein 3


Theoretical massNumber of molelcules
Total (without water)57,1742
Polymers57,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-7 kcal/mol
Surface area19780 Å2
MethodPISA
2
C: Enhancer of mRNA-decapping protein 3

C: Enhancer of mRNA-decapping protein 3


Theoretical massNumber of molelcules
Total (without water)57,1742
Polymers57,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3750 Å2
ΔGint-6 kcal/mol
Surface area19720 Å2
MethodPISA
3
D: Enhancer of mRNA-decapping protein 3

D: Enhancer of mRNA-decapping protein 3


Theoretical massNumber of molelcules
Total (without water)57,1742
Polymers57,1742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area3720 Å2
ΔGint-6 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.377, 169.204, 163.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 258 - 506 / Label seq-ID: 9 - 257

Dom-IDAuth asym-IDLabel asym-ID
1AA
2DD

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Components

#1: Protein
Enhancer of mRNA-decapping protein 3 / YjeF domain-containing protein 1 / LSM16 homolog


Mass: 28587.133 Da / Num. of mol.: 4 / Fragment: C-terminal, UNP residues 250-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDC3 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96F86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 66636 / Num. obs: 63120
Reflection shellHighest resolution: 2.2 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.267 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 3376 5.1 %RANDOM
Rwork0.22767 ---
obs0.22909 63120 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2--0.79 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 0 348 7556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227380
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.97810036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50924.11292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.739151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0681536
X-RAY DIFFRACTIONr_chiral_restr0.0760.21160
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025492
X-RAY DIFFRACTIONr_nbd_refined0.1860.23263
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2413
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.218
X-RAY DIFFRACTIONr_mcbond_it0.5571.54845
X-RAY DIFFRACTIONr_mcangle_it0.9727552
X-RAY DIFFRACTIONr_scbond_it1.22332910
X-RAY DIFFRACTIONr_scangle_it1.9614.52484
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1796 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.320.5
medium thermal0.442
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 252 -
Rwork0.253 4556 -
obs--100 %
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)
11.45441.1078-0.36491.948-0.3860.7524-0.0407-0.1311-0.1706-0.0150.0172-0.20430.05370.23410.0235-0.0691-0.00390.00750.02180.0025-0.03813.775639.474467.3719
21.18760.92030.1481.43650.38870.6325-0.0058-0.02780.1063-0.0419-0.01760.1461-0.0057-0.08280.0234-0.0583-0.0175-0.0097-0.02810.0117-0.0272-13.770742.403167.387
30.97430.1275-0.87740.4759-0.56552.1458-0.04380.05750.0274-0.0279-0.00220.06650.1203-0.0960.0461-0.0857-0.01470.0117-0.0469-0.01370.005933.349668.960241.4316
41.18130.17030.93190.63040.57882.2445-0.04970.08010.0041-0.02580.0154-0.0613-0.1380.09280.0343-0.0996-0.0147-0.01-0.05590.0080.0006-33.363412.948241.4171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA258 - 2649 - 15
2X-RAY DIFFRACTION1AA268 - 32319 - 74
3X-RAY DIFFRACTION1AA333 - 44784 - 198
4X-RAY DIFFRACTION1AA453 - 507204 - 258
5X-RAY DIFFRACTION2BB258 - 2649 - 15
6X-RAY DIFFRACTION2BB268 - 32319 - 74
7X-RAY DIFFRACTION2BB333 - 44784 - 198
8X-RAY DIFFRACTION2BB453 - 507204 - 258
9X-RAY DIFFRACTION3CC258 - 2649 - 15
10X-RAY DIFFRACTION3CC268 - 32319 - 74
11X-RAY DIFFRACTION3CC333 - 44784 - 198
12X-RAY DIFFRACTION3CC453 - 507204 - 258
13X-RAY DIFFRACTION4DD258 - 2649 - 15
14X-RAY DIFFRACTION4DD268 - 32319 - 74
15X-RAY DIFFRACTION4DD333 - 44784 - 198
16X-RAY DIFFRACTION4DD453 - 507204 - 258

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