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- PDB-5cd8: Crystal structure of the NTD of Drosophila Oskar protein -

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Basic information

Entry
Database: PDB / ID: 5cd8
TitleCrystal structure of the NTD of Drosophila Oskar protein
ComponentsMaternal effect protein oskar
KeywordsRNA BINDING PROTEIN / 3'-UTR / dimerization
Function / homology
Function and homology information


posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / posterior cell cortex / thermosensory behavior / pole plasm assembly ...posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / posterior cell cortex / thermosensory behavior / pole plasm assembly / segmentation / P granule organization / pole cell formation / visual behavior / P granule / germ cell nucleus / cortical actin cytoskeleton organization / oogenesis / germ cell development / protein localization to nucleus / long-term memory / regulation of mRNA stability / visual learning / cell cortex / endosome / mRNA binding / cytoplasm
Similarity search - Function
OSK domain / OSK domain / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / SGNH hydrolase superfamily
Similarity search - Domain/homology
Maternal effect protein oskar
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsYang, N. / Hu, M. / Yu, Z. / Wang, M. / Lehmann, R. / Xu, R.M.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370734 China
National Natural Science Foundation of China31400670 China
MOST2015CB856201 China
National Key New Drug Creation and Manufacturing Program2014ZX09507002 China
CASXDB08010100 China
CASKJZDEW-L05 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of Drosophila Oskar reveals a novel RNA binding protein
Authors: Yang, N. / Yu, Z. / Hu, M. / Wang, M. / Lehmann, R. / Xu, R.M.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maternal effect protein oskar
B: Maternal effect protein oskar
C: Maternal effect protein oskar
D: Maternal effect protein oskar
E: Maternal effect protein oskar
F: Maternal effect protein oskar
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5778
Polymers62,3926
Non-polymers1842
Water1267
1
A: Maternal effect protein oskar
B: Maternal effect protein oskar
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8903
Polymers20,7972
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Maternal effect protein oskar
D: Maternal effect protein oskar
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8903
Polymers20,7972
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Maternal effect protein oskar
F: Maternal effect protein oskar


Theoretical massNumber of molelcules
Total (without water)20,7972
Polymers20,7972
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.951, 66.951, 112.831
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Maternal effect protein oskar


Mass: 10398.719 Da / Num. of mol.: 6 / Fragment: UNP residues 150-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: osk, CG10901 / Plasmid: pET28a-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P25158
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 20% PEG 400, 200mM Mg(AC)2, 100mM NaAC, pH 5.6 / PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9641 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 11302 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 79.8 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.051 / Net I/av σ(I): 31.206 / Net I/σ(I): 12.5 / Num. measured all: 65587
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3-3.115.80.4564.111201.00799.7
3.11-3.235.80.3611361.06799.7
3.23-3.385.80.21211411.07999.9
3.38-3.565.80.13811211.08999.8
3.56-3.785.80.10311161.08699.8
3.78-4.075.80.07811211.06699.8
4.07-4.485.80.06111591.12299.8
4.48-5.135.80.05811391.08499.9
5.13-6.465.60.04411140.939100
6.46-505.80.02211350.96799.1

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHENIX(phenix.refine: 1.7.1_743)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CD7

5cd7


Resolution: 3.001→40.434 Å / FOM work R set: 0.7931 / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 2.21 / Phase error: 27.84 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 538 4.78 %Random selection
Rwork0.1893 10715 --
obs0.1918 11253 99.54 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.081 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 212.7 Å2 / Biso mean: 111.15 Å2 / Biso min: 37.38 Å2
Baniso -1Baniso -2Baniso -3
1-12.396 Å20 Å2-0 Å2
2--12.396 Å20 Å2
3----24.792 Å2
Refinement stepCycle: final / Resolution: 3.001→40.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 12 7 3461
Biso mean--124.9 61.57 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053518
X-RAY DIFFRACTIONf_angle_d0.9134762
X-RAY DIFFRACTIONf_chiral_restr0.068551
X-RAY DIFFRACTIONf_plane_restr0.004620
X-RAY DIFFRACTIONf_dihedral_angle_d15.5531324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0012-3.30310.30711390.246226812820100
3.3031-3.78080.26231210.22012669279099
3.7808-4.76220.22941530.166826912844100
4.7622-40.43770.22881250.17992674279999
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)
19.49290.5991.65229.21382.635210.0712-0.02130.256-0.3490.39650.0228-0.34430.7280.20440.12580.43390.20060.01150.31620.01030.319432.8259-28.84637.8417
212.29820.1993-0.09068.7348-7.245111.864-0.0119-0.22990.14120.32830.55150.63390.8782-0.2762-0.28580.2941-0.06610.03360.58660.10240.331231.5251-23.544-13.9408
38.3955-4.58591.30188.27540.70679.7321-0.0102-0.23580.396-0.7320.4046-0.0312-0.93520.4492-0.33391.0726-0.3739-0.02020.88070.07310.496832.1758-47.5495-29.3003
47.78420.45730.68448.98923.51118.9520.0588-0.86530.1648-0.16810.9250.936-0.25-1.1269-0.86180.97280.29070.0070.97420.18980.559631.7834-53.1754-7.1895
56.20031.6367-1.7948.10391.43446.2795-0.0463-0.4618-0.74490.18420.51360.57980.1350.5177-0.40320.942-0.1688-0.05321.19550.20730.73339.8237-36.794218.2354
65.41.57542.99279.70914.69639.59840.98140.0577-1.20730.101-0.4822-0.30530.47330.2886-0.45790.91710.1241-0.23610.8530.03230.72624.5184-39.7766-3.4964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A148 - 223
2X-RAY DIFFRACTION2chain 'B'B148 - 221
3X-RAY DIFFRACTION3chain 'C'C148 - 221
4X-RAY DIFFRACTION4chain 'D'D148 - 220
5X-RAY DIFFRACTION5chain 'E'E152 - 221
6X-RAY DIFFRACTION6chain 'F'F148 - 220

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