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- PDB-3dm1: Crystal structure of the complex of human chromobox homolog 3 (CB... -

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Basic information

Entry
Database: PDB / ID: 3dm1
TitleCrystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide
Components
  • Chromobox protein homolog 3
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
KeywordsTRANSCRIPTION / Chromobox homolog 3 / Structural Genomics / Structural Genomics Consortium / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription regulation
Function / homology
Function and homology information


regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / chromatin lock complex / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity ...regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / chromatin lock complex / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / histone methyltransferase binding / condensed chromosome, centromeric region / DNA methylation-dependent heterochromatin formation / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / cellular response to cocaine / nuclear inner membrane / negative regulation of gene expression via chromosomal CpG island methylation / organ growth / Transcriptional Regulation by E2F6 / regulation of DNA replication / site of DNA damage / RNA Polymerase I Transcription Initiation / behavioral response to cocaine / chromosome, centromeric region / Transcriptional Regulation by VENTX / spermatid development / heterochromatin / pericentric heterochromatin / long-term memory / heterochromatin formation / response to fungicide / methylated histone binding / cellular response to starvation / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / RNA polymerase II transcription regulatory region sequence-specific DNA binding / euchromatin / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / spindle / RNA polymerase II transcription regulator complex / rhythmic process / p53 binding / cellular response to xenobiotic stimulus / chromatin organization / nuclear envelope / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / chromosome, telomeric region / nuclear speck / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromobox protein homologue 3 / Histone-lysine N-methyltransferase EHMT2 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Chromo domain subgroup / Pre-SET domain ...Chromobox protein homologue 3 / Histone-lysine N-methyltransferase EHMT2 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Chromo domain subgroup / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / 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 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromobox protein homolog 3 / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.4 Å
AuthorsAmaya, M.F. / Ravichandran, M. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Amaya, M.F. / Ravichandran, M. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2012
Title: Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a.
Authors: Ruan, J. / Ouyang, H. / Amaya, M.F. / Ravichandran, M. / Loppnau, P. / Min, J. / Zang, J.
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 3
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
C: Chromobox protein homolog 3
D: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
E: Chromobox protein homolog 3
F: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
G: Chromobox protein homolog 3
H: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3


Theoretical massNumber of molelcules
Total (without water)33,1988
Polymers33,1988
Non-polymers00
Water1,63991
1
A: Chromobox protein homolog 3
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3


Theoretical massNumber of molelcules
Total (without water)8,3002
Polymers8,3002
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-6.4 kcal/mol
Surface area4180 Å2
MethodPISA
2
C: Chromobox protein homolog 3
D: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3


Theoretical massNumber of molelcules
Total (without water)8,3002
Polymers8,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-8.6 kcal/mol
Surface area4360 Å2
MethodPISA
3
E: Chromobox protein homolog 3
F: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3


Theoretical massNumber of molelcules
Total (without water)8,3002
Polymers8,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-7.7 kcal/mol
Surface area4280 Å2
MethodPISA
4
G: Chromobox protein homolog 3
H: Histone-lysine N-methyltransferase, H3 lysine-9 specific 3


Theoretical massNumber of molelcules
Total (without water)8,3002
Polymers8,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area4350 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-62.1 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.671, 83.671, 110.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Chromobox protein homolog 3 / Heterochromatin protein 1 homolog gamma / HP1 gamma / Modifier 2 protein / HECH


Mass: 6812.642 Da / Num. of mol.: 4 / Fragment: Chromo 1 domain: Residues 29-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q13185
#2: Protein/peptide
Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 / Histone H3-K9 methyltransferase 3 / H3-K9-HMTase 3 / Euchromatic histone-lysine N-methyltransferase ...Histone H3-K9 methyltransferase 3 / H3-K9-HMTase 3 / Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Protein G9a / Lysine N-methyltransferase 1C


Mass: 1486.870 Da / Num. of mol.: 4 / Fragment: UNP residues 179-190 / Source method: obtained synthetically
Details: Synthetic peptide with the sequence matching the residues 179-190 of the human histone H3-K9 methyltransferase 3, EHMT2_HUMAN, UNP entry Q96KQ7
References: UniProt: Q96KQ7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.28268 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28268 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 17856 / % possible obs: 99.9 % / Redundancy: 10.52 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 24.63
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 4.38 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→39.1 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.89 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26725 908 5.1 %RANDOM
Rwork0.21951 ---
obs0.2219 17856 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.532 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 91 2101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9532792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05724.643112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95615342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5591514
X-RAY DIFFRACTIONr_chiral_restr0.1180.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021562
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2766
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21357
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2780.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.51251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07221952
X-RAY DIFFRACTIONr_scbond_it2.7843941
X-RAY DIFFRACTIONr_scangle_it4.2114.5839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 76 -
Rwork0.27 1218 -
obs--99.62 %

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