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- PDB-4quf: crystal structure of chromodomain of Rhino with H3K9me3 -

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Basic information

Entry
Database: PDB / ID: 4quf
Titlecrystal structure of chromodomain of Rhino with H3K9me3
Components
  • H3(1-15)K9me3 peptide
  • RE36324p
KeywordsPROTEIN BINDING / piRNA biogensis / histone binding
Function / homology
Function and homology information


piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / piRNA processing / chromosome organization / heterochromatin / pericentric heterochromatin / : ...piRNA transcription / positive regulation of piRNA transcription / Rhino-Deadlock-Cutoff Complex / positive regulation of snRNA transcription by RNA polymerase II / chorion-containing eggshell pattern formation / piRNA processing / chromosome organization / heterochromatin / pericentric heterochromatin / : / transcription antitermination / heterochromatin formation / chromatin binding / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / : / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...: / : / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromo domain-containing protein rhino
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsLi, S. / Patel, D.J.
CitationJournal: Genes Dev. / Year: 2014
Title: Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing.
Authors: Le Thomas, A. / Stuwe, E. / Li, S. / Du, J. / Marinov, G. / Rozhkov, N. / Chen, Y.C. / Luo, Y. / Sachidanandam, R. / Toth, K.F. / Patel, D. / Aravin, A.A.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RE36324p
P: H3(1-15)K9me3 peptide
B: RE36324p
Q: H3(1-15)K9me3 peptide
C: RE36324p
R: H3(1-15)K9me3 peptide
D: RE36324p
T: H3(1-15)K9me3 peptide
E: RE36324p
V: H3(1-15)K9me3 peptide
F: RE36324p
U: H3(1-15)K9me3 peptide


Theoretical massNumber of molelcules
Total (without water)56,96312
Polymers56,96312
Non-polymers00
Water3,657203
1
A: RE36324p
P: H3(1-15)K9me3 peptide
B: RE36324p
Q: H3(1-15)K9me3 peptide


Theoretical massNumber of molelcules
Total (without water)18,9884
Polymers18,9884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-19 kcal/mol
Surface area8020 Å2
MethodPISA
2
C: RE36324p
R: H3(1-15)K9me3 peptide
D: RE36324p
T: H3(1-15)K9me3 peptide


Theoretical massNumber of molelcules
Total (without water)18,9884
Polymers18,9884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-19 kcal/mol
Surface area8090 Å2
MethodPISA
3
E: RE36324p
V: H3(1-15)K9me3 peptide
F: RE36324p
U: H3(1-15)K9me3 peptide


Theoretical massNumber of molelcules
Total (without water)18,9884
Polymers18,9884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-19 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.317, 79.932, 81.181
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RE36324p / Rhino


Mass: 7885.945 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rhi, rhino, CG10683, Dmel_CG10683 / Plasmid: pETsumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q7JXA8
#2: Protein/peptide
H3(1-15)K9me3 peptide


Mass: 1607.877 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: peptide was synthesized at TUFTS university
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium nitrate and 20% PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 18675 / Num. obs: 18675 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 2 / Num. unique all: 1854 / Rsym value: 0.818 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QUC

4quc


Resolution: 2.501→37.216 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 951 5.1 %RANDOM
Rwork0.1948 ---
all0.1976 18675 --
obs0.1976 18648 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→37.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 0 203 3506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083368
X-RAY DIFFRACTIONf_angle_d1.2334538
X-RAY DIFFRACTIONf_dihedral_angle_d16.0891268
X-RAY DIFFRACTIONf_chiral_restr0.079476
X-RAY DIFFRACTIONf_plane_restr0.006581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5006-2.63240.32351480.25062479X-RAY DIFFRACTION99
2.6324-2.79730.30031370.25112498X-RAY DIFFRACTION100
2.7973-3.01320.34581400.23222550X-RAY DIFFRACTION100
3.0132-3.31630.24411350.2032499X-RAY DIFFRACTION100
3.3163-3.79570.24441300.17932542X-RAY DIFFRACTION100
3.7957-4.78060.22351240.15652564X-RAY DIFFRACTION100
4.7806-37.22020.20381370.19112565X-RAY DIFFRACTION100
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)
14.55131.685-2.94092.7218-1.35632.36040.2399-0.52990.17570.2055-0.3336-0.1036-0.1240.37460.04020.1513-0.0041-0.00420.27370.03490.146747.76979.79738.1243
23.41750.15420.38698.26461.32392.2822-0.11190.4242-0.2086-0.83030.32340.55790.04520.17110.08130.1481-0.0387-0.06230.2961-0.00290.229344.20255.0804-3.3747
33.5897-0.9410.69747.7941-2.04153.3565-0.24730.35050.71150.65240.31340.61680.0387-0.1308-0.27250.1673-0.068-0.06630.3501-0.01160.252846.384817.80124.7195
42.84530.1653-1.71241.7320.11792.56730.3840.15260.3219-0.6022-0.03980.54610.07640.06680.13590.10030.00770.02070.3508-0.02420.045229.5678.9815-4.3663
54.5520.3952-2.24682.91911.51534.2080.35211.28780.39360.0471-0.1720.3190.0307-0.07990.01050.1931-0.01040.00020.27010.00470.119525.593710.929-5.667
60.8576-1.3131-0.17665.4456-2.16462.0975-0.2749-0.398-0.15620.11470.3608-0.25440.0794-0.54990.07390.2041-0.0725-0.02240.41140.08770.2631.65411.59597.7487
74.78080.33211.36774.91813.69123.72870.262-0.17920.8064-0.27660.2926-0.4688-0.53870.3818-0.21580.25260.0241-0.05640.2738-0.0110.297529.195517.9732-1.3762
85.6447-0.92990.98058.0894-1.11745.3648-0.09930.1986-0.54360.07720.2976-0.91990.75880.1060.0990.3603-0.0035-0.09770.2063-0.02470.086242.1917-24.022828.4569
92.53610.06130.17631.3196-0.44921.92310.13620.2689-0.15250.2264-0.07760.18910.07930.0037-0.05880.2702-0.0337-0.01550.16350.03540.240537.265-15.400129.4632
102.3579-0.5583-2.30810.7299-1.2887.9340.4341-0.0690.29250.6064-0.1192-0.8606-0.58790.5101-0.27460.5675-0.0241-0.12370.31390.04030.366946.2324-23.488531.2692
113.76121.41142.48093.27060.20664.12990.1630.0232-0.15660.065-0.1204-0.54040.20080.0656-0.00350.18110.0238-0.00360.15570.04680.215452.244-2.44424.6242
128.2352-2.538-2.63894.47391.6044.69820.0765-0.17710.3370.42040.01720.48-0.08380.0901-0.05070.3749-0.08760.02350.16480.01290.342944.3384-4.203835.2444
136.23111.96990.0667.607-0.8199.02330.60830.1268-0.08660.34080.0537-0.29680.37030.1045-0.14960.43380.02530.04070.28580.08730.404557.6089-8.113926.2901
140.4858-0.0913-0.39735.3621.42172.0347-0.1210.0351-0.18130.23550.00190.12060.00350.2360.08150.21220.0643-0.01460.1930.01810.14849.310319.546530.4441
152.9622.3661-2.15293.3624-0.96662.5093-0.32050.21480.477-0.5030.1586-0.25080.11430.04660.47260.2883-0.0393-0.01180.25970.03870.28349.634126.669324.1882
164.09830.3999-2.37380.8363-1.25618.3497-0.3296-0.40840.21470.56580.2766-0.9053-0.80280.29130.35380.4655-0.0299-0.10620.26160.15810.3757.271918.490531.9404
172.9827-1.12042.48123.99280.64413.21640.396-0.0365-0.25430.4516-0.2994-0.4453-0.0770.43490.2760.6011-0.3246-0.25120.70610.30870.262263.8140.384927.8747
184.71180.86812.12860.7835-0.23522.444-0.1541-0.27380.0436-0.0791-0.4516-0.6210.12461.0061-0.03580.2363-0.2051-0.08260.41120.15820.302258.680140.420.8233
196.4525-2.0012-2.20365.0189-0.23333.87920.3362-0.6254-0.630.5275-0.31570.1179-0.57870.26020.16220.3646-0.0616-0.06820.19760.02240.210849.053937.71632.4537
201.8691-0.02440.10151.61720.21910.03470.21840.261-0.38-0.0586-0.0694-0.07820.06270.143-0.26340.2278-0.111-0.20940.63490.34420.752666.271933.979626.1539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 78 )
3X-RAY DIFFRACTION3chain 'P' and (resid 3 through 10 )
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 45 )
5X-RAY DIFFRACTION5chain 'B' and (resid 46 through 61 )
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 84 )
7X-RAY DIFFRACTION7chain 'Q' and (resid 3 through 10 )
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 30 )
9X-RAY DIFFRACTION9chain 'C' and (resid 31 through 82 )
10X-RAY DIFFRACTION10chain 'R' and (resid 3 through 11 )
11X-RAY DIFFRACTION11chain 'D' and (resid 22 through 61 )
12X-RAY DIFFRACTION12chain 'D' and (resid 62 through 79 )
13X-RAY DIFFRACTION13chain 'T' and (resid 4 through 10 )
14X-RAY DIFFRACTION14chain 'E' and (resid 22 through 53 )
15X-RAY DIFFRACTION15chain 'E' and (resid 54 through 79 )
16X-RAY DIFFRACTION16chain 'V' and (resid 5 through 10 )
17X-RAY DIFFRACTION17chain 'F' and (resid 23 through 30 )
18X-RAY DIFFRACTION18chain 'F' and (resid 31 through 61 )
19X-RAY DIFFRACTION19chain 'F' and (resid 62 through 82 )
20X-RAY DIFFRACTION20chain 'U' and (resid 5 through 8 )

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