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- PDB-5xyv: Crystal structure of drosophila melanogaster Rhino chromoshadow d... -

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Basic information

Entry
Database: PDB / ID: 5xyv
TitleCrystal structure of drosophila melanogaster Rhino chromoshadow domain in complex with Deadlock N-terminal domain
Components
  • Protein deadlock
  • RHINORhinoceros
KeywordsPROTEIN BINDING / piRNA pathway / Chromoshadow / Complex
Function / homology
Function and homology information


piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / oocyte localization involved in germarium-derived egg chamber formation / heterochromatin => GO:0000792 / germarium-derived egg chamber formation / fusome organization / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / oocyte karyosome formation ...piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / oocyte localization involved in germarium-derived egg chamber formation / heterochromatin => GO:0000792 / germarium-derived egg chamber formation / fusome organization / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / oocyte karyosome formation / piRNA processing / multicellular organism development / oocyte development / oogenesis / chromosome organization / heterochromatin / pericentric heterochromatin / methylated histone binding / mitotic spindle organization / transcription antitermination / chromatin organization / centrosome / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
: / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
RHINO / Chromo domain-containing protein rhino / Protein deadlock
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYu, B.W. / Huang, Y.
CitationJournal: EMBO Rep. / Year: 2018
Title: Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification
Authors: Yu, B. / Lin, Y.A. / Parhad, S.S. / Jin, Z. / Ma, J. / Theurkauf, W.E. / Zhang, Z.Z. / Huang, Y.
History
DepositionJul 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 22, 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: RHINO
B: RHINO
C: Protein deadlock
D: Protein deadlock


Theoretical massNumber of molelcules
Total (without water)31,3704
Polymers31,3704
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-52 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.752, 57.097, 101.002
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 RHINO / Rhinoceros


Mass: 8577.806 Da / Num. of mol.: 2 / Fragment: UNP residues 353-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rhi / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L0CPQ5, UniProt: Q7JXA8*PLUS
#2: Protein Protein deadlock


Mass: 7107.214 Da / Num. of mol.: 2 / Fragment: UNP residues 1-60
Source method: isolated from a genetically manipulated source
Details: In the electron density maps we only observed the main chain of 45R, so we used Alanine instead.
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: del, CG9252 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VIF5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25%(W/V) PEG3350, 0.1 M HEPES (pH 7.5), 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 16741 / % possible obs: 99.4 % / Redundancy: 8.1 % / Net I/σ(I): 22.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 16741 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMM

2fmm


Resolution: 2.1→29.651 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2532 1675 10.01 %
Rwork0.2126 --
obs0.2166 16741 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 0 110 1931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091867
X-RAY DIFFRACTIONf_angle_d1.2712517
X-RAY DIFFRACTIONf_dihedral_angle_d16.955682
X-RAY DIFFRACTIONf_chiral_restr0.053273
X-RAY DIFFRACTIONf_plane_restr0.005308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0947-2.15630.30791310.31211187X-RAY DIFFRACTION96
2.1563-2.22590.35041370.31331224X-RAY DIFFRACTION99
2.2259-2.30540.36261370.29031235X-RAY DIFFRACTION99
2.3054-2.39770.31771390.27291247X-RAY DIFFRACTION99
2.3977-2.50670.32911370.24871238X-RAY DIFFRACTION100
2.5067-2.63880.29771380.23261241X-RAY DIFFRACTION100
2.6388-2.8040.2681390.21771247X-RAY DIFFRACTION100
2.804-3.02030.27061400.22671260X-RAY DIFFRACTION99
3.0203-3.32390.28091380.20471254X-RAY DIFFRACTION100
3.3239-3.8040.21851430.17741273X-RAY DIFFRACTION100
3.804-4.78940.17751430.16381296X-RAY DIFFRACTION100
4.7894-29.65430.21521530.18671364X-RAY DIFFRACTION100

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