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- PDB-5cff: Crystal structure of Miranda/Staufen dsRBD5 complex -

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Basic information

Entry
Database: PDB / ID: 5cff
TitleCrystal structure of Miranda/Staufen dsRBD5 complex
Components
  • Miranda
  • Staufen
KeywordsTRANSCRIPTION/RNA BINDING PROTEIN / Coiled-coil and dsRNA-binding domain complex / TRANSCRIPTION-RNA BINDING PROTEIN complex
Function / homology
Function and homology information


germ plasm / regulation of intracellular mRNA localization / subsynaptic reticulum / pole plasm RNA localization / ganglion mother cell fate determination / bicoid mRNA localization / regulation of oskar mRNA translation / pole plasm protein localization / posterior cell cortex / regulation of pole plasm oskar mRNA localization ...germ plasm / regulation of intracellular mRNA localization / subsynaptic reticulum / pole plasm RNA localization / ganglion mother cell fate determination / bicoid mRNA localization / regulation of oskar mRNA translation / pole plasm protein localization / posterior cell cortex / regulation of pole plasm oskar mRNA localization / asymmetric protein localization involved in cell fate determination / protein localization to cell cortex / anterograde dendritic transport of messenger ribonucleoprotein complex / positive regulation of cytoplasmic mRNA processing body assembly / neuroblast fate determination / pole plasm assembly / positive regulation of synaptic assembly at neuromuscular junction / ventral cord development / neuronal ribonucleoprotein granule / RNA localization / basal cortex / anterior/posterior axis specification, embryo / asymmetric neuroblast division / intracellular mRNA localization / apical cortex / basal part of cell / protein localization to synapse / oogenesis / lncRNA binding / myosin binding / germ cell development / regulation of proteolysis / neuroblast proliferation / long-term memory / dendrite cytoplasm / basal plasma membrane / mRNA 3'-UTR binding / P-body / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / apical part of cell / double-stranded RNA binding / cell cortex / neuron projection / apical plasma membrane / neuronal cell body / mRNA binding / centrosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
Staufen, C-terminal / : / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Maternal effect protein staufen / Miranda, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShan, Z. / Wen, W.
CitationJournal: Nat Commun / Year: 2015
Title: The structural basis of Miranda-mediated Staufen localization during Drosophila neuroblast asymmetric division
Authors: Jia, M. / Shan, Z. / Yang, Y. / Liu, C. / Li, J. / Luo, Z.G. / Zhang, M. / Cai, Y. / Wen, W. / Wang, W.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Miranda
B: Miranda
C: Miranda
D: Miranda
E: Staufen
F: Staufen
G: Staufen
H: Staufen


Theoretical massNumber of molelcules
Total (without water)74,6988
Polymers74,6988
Non-polymers00
Water48627
1
A: Miranda
C: Miranda
F: Staufen
H: Staufen


Theoretical massNumber of molelcules
Total (without water)37,3494
Polymers37,3494
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-76 kcal/mol
Surface area16700 Å2
MethodPISA
2
B: Miranda
D: Miranda
E: Staufen
G: Staufen


Theoretical massNumber of molelcules
Total (without water)37,3494
Polymers37,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-73 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.023, 51.332, 100.274
Angle α, β, γ (deg.)90.000, 90.560, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
12chain E
22chain F
32chain G
42chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSERchain AAA503 - 5893 - 89
21GLYGLYSERSERchain BBB501 - 5881 - 88
31PROPROSERSERchain CCC502 - 5882 - 88
41PROPROSERSERchain DDD502 - 5892 - 89
12GLYGLYLEULEUchain EEE949 - 10183 - 72
22PROPROLEULEUchain FFF948 - 10182 - 72
32GLYGLYLEULEUchain GGG949 - 10183 - 72
42GLYGLYLEULEUchain HHH949 - 10183 - 72

NCS ensembles :
ID
1
2

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Components

#1: Protein
Miranda


Mass: 10729.630 Da / Num. of mol.: 4 / Fragment: UNP residues 514-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: mira, CG12249, Dmel_CG12249 / Plasmid: pET.32M.3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9VDR7
#2: Protein
Staufen


Mass: 7944.774 Da / Num. of mol.: 4
Fragment: The fifth dsRNA-binding domain, UNP residues 953-1019
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: stau, CG5753 / Plasmid: pET.32M.3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P25159
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.61 Å3/Da / Density % sol: 65.91 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: sodium acetate,1,6-hexanediol,calcium chloride etc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 5.5 % / Number: 189671 / Rmerge(I) obs: 0.078 / Χ2: 2.49 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 34191 / % possible obs: 94.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.785010.0453.8654.8
5.386.7810.0553.9495.4
4.75.3810.0483.665.7
4.274.710.053.3715.9
3.974.2710.0553.3035.5
3.733.9710.0693.9892.4
3.553.7310.0763.5112.9
3.393.5510.0923.4874.7
3.263.3910.12.665.6
3.153.2610.1212.2546
3.053.1510.1472.1396
2.963.0510.1771.9826
2.892.9610.2071.8956
2.822.8910.2571.7696.1
2.752.8210.3121.7296.1
2.692.7510.441.7825.9
2.642.6910.4322.5995.6
2.592.6410.6761.7245.9
2.542.5910.6381.5286.1
2.52.5410.6641.6016.1
ReflectionResolution: 2.5→50 Å / Num. obs: 34191 / % possible obs: 94.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 53.81 Å2 / Rmerge(I) obs: 0.078 / Χ2: 2.488 / Net I/av σ(I): 35.389 / Net I/σ(I): 13.9 / Num. measured all: 189671
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.546.10.66417801.60199.8
2.54-2.596.10.63818071.52899.9
2.59-2.645.90.67617641.72499.6
2.64-2.695.60.43217732.59999.6
2.69-2.755.90.4417901.78299.8
2.75-2.826.10.31217801.72999.9
2.82-2.896.10.25717921.76999.9
2.89-2.9660.20717771.89599.9
2.96-3.0560.17718031.98299.8
3.05-3.1560.14717622.13999.8
3.15-3.2660.12117892.25499.8
3.26-3.395.60.117692.6699.5
3.39-3.554.70.09217563.48797.8
3.55-3.732.90.07610373.51157.3
3.73-3.972.40.06911213.98961.7
3.97-4.275.50.05517493.30397.3
4.27-4.75.90.0518253.37199.8
4.7-5.385.70.04817953.6699.4
5.38-6.785.40.05518373.94999.8
6.78-504.80.04516853.86588.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SHELXphasing
DMphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→27.664 Å / FOM work R set: 0.7235 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.26 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.281 1696 5.02 %
Rwork0.2423 32081 -
obs0.2443 33777 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.78 Å2 / Biso mean: 42.57 Å2 / Biso min: 14.05 Å2
Refinement stepCycle: final / Resolution: 2.5→27.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4591 0 0 27 4618
Biso mean---33.19 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014656
X-RAY DIFFRACTIONf_angle_d1.1836309
X-RAY DIFFRACTIONf_chiral_restr0.053772
X-RAY DIFFRACTIONf_plane_restr0.006812
X-RAY DIFFRACTIONf_dihedral_angle_d15.9471648
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1440X-RAY DIFFRACTION12.008TORSIONAL
12B1440X-RAY DIFFRACTION12.008TORSIONAL
13C1440X-RAY DIFFRACTION12.008TORSIONAL
14D1440X-RAY DIFFRACTION12.008TORSIONAL
21E1143X-RAY DIFFRACTION12.008TORSIONAL
22F1143X-RAY DIFFRACTION12.008TORSIONAL
23G1143X-RAY DIFFRACTION12.008TORSIONAL
24H1143X-RAY DIFFRACTION12.008TORSIONAL
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 (%)
2.4929-2.56620.35171590.32052767292697
2.5662-2.64890.42491280.35422701282996
2.6489-2.74350.45151360.36492761289797
2.7435-2.85330.42181660.31942790295699
2.8533-2.9830.36881520.29322768292099
2.983-3.14010.32511350.27982827296299
3.1401-3.33650.34691250.29482805293098
3.3365-3.59360.32641310.2552738286996
3.5936-3.95430.3225780.25661510158853
3.9543-4.52430.23651640.18772773293798
4.5243-5.6920.21021630.192928653028100
5.692-27.66540.23071590.2142776293594

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