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- PDB-2vxg: Crystal structure of the conserved C-terminal region of Ge-1 -

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Basic information

Entry
Database: PDB / ID: 2vxg
TitleCrystal structure of the conserved C-terminal region of Ge-1
ComponentsCG6181-PA, ISOFORM A
KeywordsGENE REGULATION / DECAPPING / EDC4 / HEDLS / MRNA DECAY / P-BODY
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / pole plasm oskar mRNA localization / deadenylation-independent decapping of nuclear-transcribed mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / miRNA-mediated post-transcriptional gene silencing / P-body assembly / mRNA catabolic process / defense response to fungus / P-body
Similarity search - Function
conserved c-terminal region of ge- 1 / Helix Hairpins - #270 / Enhancer of mRNA-decapping protein 4, WD40 repeat region / WD40 region of Ge1, enhancer of mRNA-decapping protein / Annexin V; domain 1 / Helix Hairpins / Helix non-globular / Special / Trp-Asp (WD) repeats signature. / WD40 repeats ...conserved c-terminal region of ge- 1 / Helix Hairpins - #270 / Enhancer of mRNA-decapping protein 4, WD40 repeat region / WD40 region of Ge1, enhancer of mRNA-decapping protein / Annexin V; domain 1 / Helix Hairpins / Helix non-globular / Special / Trp-Asp (WD) repeats signature. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Enhancer of mRNA-decapping protein 4 homolog
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJinek, M. / Eulalio, A. / Lingel, A. / Helms, S. / Conti, E. / Izaurralde, E.
CitationJournal: RNA / Year: 2008
Title: The C-Terminal Region of Ge-1 Presents Conserved Structural Features Required for P-Body Localization.
Authors: Jinek, M. / Eulalio, A. / Lingel, A. / Helms, S. / Conti, E. / Izaurralde, E.
History
DepositionJul 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG6181-PA, ISOFORM A
B: CG6181-PA, ISOFORM A


Theoretical massNumber of molelcules
Total (without water)31,6002
Polymers31,6002
Non-polymers00
Water2,846158
1
A: CG6181-PA, ISOFORM A


Theoretical massNumber of molelcules
Total (without water)15,8001
Polymers15,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CG6181-PA, ISOFORM A


Theoretical massNumber of molelcules
Total (without water)15,8001
Polymers15,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.240, 65.870, 103.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CG6181-PA, ISOFORM A / LD41624 / GE-1


Mass: 15800.232 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1220-1354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETM-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9VKK1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEQUENCE GAM DERIVED FROM EXPRESSION VECTOR

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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: 2.07 Å3/Da / Density % sol: 40.6 % / Description: NONE
Crystal growpH: 8.2 / Details: 100 MM TRIS-CL PH 8.2 21% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97897
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 1.9→55.6 Å / Num. obs: 20948 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→55.64 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.755 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1048 5 %RANDOM
Rwork0.211 ---
obs0.213 19899 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: 17.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.74 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→55.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 0 158 2206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222079
X-RAY DIFFRACTIONr_bond_other_d0.0030.021402
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9642800
X-RAY DIFFRACTIONr_angle_other_deg1.00933446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61125.25399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50315399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8821512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_nbd_refined0.2340.2527
X-RAY DIFFRACTIONr_nbd_other0.1740.21466
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21010
X-RAY DIFFRACTIONr_nbtor_other0.0890.21054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2721.51714
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37222067
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4823863
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5614.5732
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 67
Rwork0.239 1262
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)
11.036-0.31440.70890.1217-0.17131.8549-0.03440.00970.0973-0.0182-0.0093-0.1069-0.23240.02970.04370.0006-0.00720.0044-0.0134-0.0195-0.04230.88264.61812.757
20.3360.0901-0.07971.32461.25722.0111-0.0363-0.0497-0.05090.0580.1117-0.01710.00990.0371-0.0754-0.02610.0439-0.0295-0.01430.0187-0.062928.94461.20437.532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1216 - 1350
2X-RAY DIFFRACTION2B1216 - 1350

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