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- PDB-5cd7: Crystal structure of the NTD L199M of Drosophila Oskar protein -

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Basic information

Entry
Database: PDB / ID: 5cd7
TitleCrystal structure of the NTD L199M 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 / P granule organization ...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 / P granule organization / pole plasm assembly / segmentation / 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 / SAD / Resolution: 2.502 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
MOST2015CB856202 China
National Key New Drog 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 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)52,11010
Polymers51,7416
Non-polymers3684
Water73941
1
A: Maternal effect protein oskar
B: Maternal effect protein oskar
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5235
Polymers17,2472
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Maternal effect protein oskar
D: Maternal effect protein oskar


Theoretical massNumber of molelcules
Total (without water)17,2472
Polymers17,2472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Maternal effect protein oskar
F: Maternal effect protein oskar
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3393
Polymers17,2472
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.962, 38.307, 102.130
Angle α, β, γ (deg.)90.000, 95.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Maternal effect protein oskar


Mass: 8623.562 Da / Num. of mol.: 6 / Fragment: UNP residues 150-224 / Mutation: L199M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: osk, CG10901 / Production host: Escherichia coli (E. coli) / References: UniProt: P25158
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 17-22% PEG 3350, 150mM NaCl, 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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 34100 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 53.07 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.339 / Net I/av σ(I): 26.333 / Net I/σ(I): 12.4 / Num. measured all: 124860
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.597.50.4284.916871.012100
2.59-2.697.50.32916771.092100
2.69-2.827.50.24616841.13100
2.82-2.967.50.20217101.20899.9
2.96-3.157.40.13216801.22999.9
3.15-3.397.40.09716931.28599.9
3.39-3.7370.08417001.15899.5
3.73-4.277.30.07917141.31199.8
4.27-5.387.20.06317161.4799.8
5.38-5070.04917932.50699.4

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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
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.502→37.734 Å / FOM work R set: 0.7343 / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 32.52 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 1629 5.02 %Random selection
Rwork0.2143 30804 --
obs0.2172 32433 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.844 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso max: 243.89 Å2 / Biso mean: 89.11 Å2 / Biso min: 27.36 Å2
Baniso -1Baniso -2Baniso -3
1-6.9545 Å20 Å2-5.311 Å2
2--5.8641 Å20 Å2
3----12.8186 Å2
Refinement stepCycle: final / Resolution: 2.502→37.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 24 41 3446
Biso mean--80.19 60.09 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053465
X-RAY DIFFRACTIONf_angle_d0.94680
X-RAY DIFFRACTIONf_chiral_restr0.069541
X-RAY DIFFRACTIONf_plane_restr0.003606
X-RAY DIFFRACTIONf_dihedral_angle_d14.5251310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5023-2.5760.32811460.28672349249590
2.576-2.65910.32921380.253225712709100
2.6591-2.75410.33681270.25522645277299
2.7541-2.86430.33371160.260525542670100
2.8643-2.99460.33091290.259726092738100
2.9946-3.15240.25391290.236725852714100
3.1524-3.34980.26411210.25326052726100
3.3498-3.60830.31821200.24322570269099
3.6083-3.97110.27241560.225325912747100
3.9711-4.54480.23751570.179125702727100
4.5448-5.72280.26321440.187226092753100
5.7228-37.73830.24451460.18692546269299
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)
16.49411.9284-0.73794.90420.31537.50780.1662-0.54780.14480.1466-0.008-0.0336-0.0425-0.2312-0.14410.3808-0.0256-0.07310.2031-0.0530.203256.11284.24034.3426
26.8695-3.5377-0.55677.6870.25878.9870.037-1.0150.77770.41430.3514-0.2042-0.2478-0.3089-0.41240.4927-0.0680.03180.6246-0.09790.326757.90765.89626.6115
36.22141.156-0.25855.43420.13734.55060.2150.33780.62131.1199-0.2307-0.4248-0.17020.60370.0680.79560.0831-0.27310.65210.10620.456425.25213.1417-22.8107
47.55850.47263.89824.36130.26075.21480.393-0.4176-0.5036-0.3170.04610.86830.291-1.5015-0.05950.6065-0.227-0.29490.74250.12120.439238.7911-1.5355-4.7595
57.1003-1.40283.37283.7858-0.16657.26330.419-1.4026-1.0813-0.1376-0.3923-0.02290.79361.2786-0.26310.95510.0608-0.31071.41650.2560.534170.4779-5.423839.678
63.68441.12562.74670.57520.12814.2667-0.0612.11490.0319-0.78690.3881-0.01480.45271.5488-0.20460.5934-0.0531-0.14841.92240.10720.464481.7371-2.056658.8912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A148 - 224
2X-RAY DIFFRACTION2chain 'B'B150 - 221
3X-RAY DIFFRACTION3chain 'C'C148 - 222
4X-RAY DIFFRACTION4chain 'D'D149 - 221
5X-RAY DIFFRACTION5chain 'E'E154 - 221
6X-RAY DIFFRACTION6chain 'F'F155 - 222

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