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- PDB-4u68: Crystal structure of Rhino chromodomain in complex with H3K9me3 -

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Basic information

Entry
Database: PDB / ID: 4u68
TitleCrystal structure of Rhino chromodomain in complex with H3K9me3
Components
  • H3K9me3
  • Rhino
KeywordsPROTEIN BINDING / Rhino / H3K9me3 / piRNA
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 / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / SIRT1 negatively regulates rRNA expression ...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 / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / piRNA processing / polytene chromosome / chromosome organization / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / epigenetic regulation of gene expression / nucleosomal DNA binding / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / transcription antitermination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / Histone H3 signature 1. / Histone H3 signature 2. ...: / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H3 / Histone H3.1 / Chromo domain-containing protein rhino
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYu, B.W. / Huang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2012CB910502 China
National Natural Science Foundation of China31270774 China
Strategic Priority Research ProgramXDB08010202 China
CitationJournal: Cell Res. / Year: 2015
Title: Structural insights into Rhino-mediated germline piRNA cluster formation
Authors: Yu, B.W. / Cassani, M. / Wang, M. / Liu, M. / Ma, J. / Li, G. / Zhang, Z. / Huang, Y.
History
DepositionJul 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Oct 23, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list / reflns_shell
Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.Rmerge_I_obs
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 2.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhino
B: Rhino
C: Rhino
D: H3K9me3
E: H3K9me3
F: H3K9me3


Theoretical massNumber of molelcules
Total (without water)28,9476
Polymers28,9476
Non-polymers00
Water3,153175
1
A: Rhino
D: H3K9me3

A: Rhino
D: H3K9me3


Theoretical massNumber of molelcules
Total (without water)19,2984
Polymers19,2984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3800 Å2
ΔGint-21 kcal/mol
Surface area8870 Å2
MethodPISA
2
B: Rhino
C: Rhino
E: H3K9me3
F: H3K9me3


Theoretical massNumber of molelcules
Total (without water)19,2984
Polymers19,2984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-22 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.946, 67.679, 79.750
Angle α, β, γ (deg.)90.00, 106.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-138-

HOH

21C-106-

HOH

31C-138-

HOH

41C-148-

HOH

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Components

#1: Protein Rhino / RE36324p


Mass: 8441.594 Da / Num. of mol.: 3 / Fragment: chromodomain, UNP residues 20-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rhi, rhino, CG10683, Dmel_CG10683 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7JXA8
#2: Protein/peptide H3K9me3


Mass: 1207.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P02299, UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30 %(v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→25.5 Å / Num. obs: 23980 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWE

3lwe


Resolution: 1.8→25.494 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 2005 8.36 %
Rwork0.1844 --
obs0.1862 23980 99.22 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→25.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 0 175 1853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081711
X-RAY DIFFRACTIONf_angle_d1.1552301
X-RAY DIFFRACTIONf_dihedral_angle_d14.47652
X-RAY DIFFRACTIONf_chiral_restr0.042242
X-RAY DIFFRACTIONf_plane_restr0.005294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.29361460.23441536X-RAY DIFFRACTION97
1.845-1.89490.24661370.21711562X-RAY DIFFRACTION100
1.8949-1.95060.23931510.20621549X-RAY DIFFRACTION99
1.9506-2.01360.2491350.18851580X-RAY DIFFRACTION99
2.0136-2.08550.19131500.18611544X-RAY DIFFRACTION100
2.0855-2.16890.19791410.1821552X-RAY DIFFRACTION100
2.1689-2.26760.23861420.17851601X-RAY DIFFRACTION100
2.2676-2.38710.21671410.18881569X-RAY DIFFRACTION100
2.3871-2.53650.21211430.18471578X-RAY DIFFRACTION100
2.5365-2.73210.24441400.1941554X-RAY DIFFRACTION100
2.7321-3.00670.22151470.18651599X-RAY DIFFRACTION100
3.0067-3.44090.18911420.17681572X-RAY DIFFRACTION100
3.4409-4.33170.17631420.16261589X-RAY DIFFRACTION100
4.3317-25.49640.19291480.19311590X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -36.1819 Å / Origin y: 26.6944 Å / Origin z: 22.7987 Å
111213212223313233
T0.0979 Å20.0226 Å20.0177 Å2-0.1061 Å20.003 Å2--0.1099 Å2
L0.6638 °2-0.4768 °20.6218 °2-0.3738 °2-0.3157 °2--0.71 °2
S0.0718 Å °-0.0166 Å °-0.0044 Å °-0.0628 Å °-0.024 Å °-0.0592 Å °-0.0122 Å °0.0148 Å °0 Å °
Refinement TLS groupSelection details: all

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