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- PDB-9cdw: Crystal structure of HP1alpha chromoshadow domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 9cdw
TitleCrystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide
Components
  • Chromobox protein homolog 5
  • Transcription intermediary factor 1-beta peptide
KeywordsTRANSCRIPTION/PEPTIDE / HP1 / CSD domain / KAP1 / TRANSCRIPTION / TRANSCRIPTION-PEPTIDE complex
Function / homology
Function and homology information


convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / suppression of viral release by host / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromocenter / genomic imprinting / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity ...convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / suppression of viral release by host / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromocenter / genomic imprinting / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity / histone methyltransferase complex / DNA methylation-dependent constitutive heterochromatin formation / Transcriptional Regulation by E2F6 / site of DNA damage / protein sumoylation / histone deacetylase complex / epithelial to mesenchymal transition / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / : / transcription repressor complex / embryo implantation / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / positive regulation of DNA repair / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / kinetochore / histone deacetylase binding / RNA polymerase II transcription regulator complex / positive regulation of protein import into nucleus / HCMV Early Events / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / nuclear envelope / heterochromatin formation / chromatin organization / Factors involved in megakaryocyte development and platelet production / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / chromosome, telomeric region / protein kinase activity / ribonucleoprotein complex / innate immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein-containing complex binding / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / B-box, C-terminal / B-Box C-terminal domain / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chromobox protein homolog 5 / Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSelvam, K. / Singh, R.K. / Gaurav, N. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: The HP1 box of KAP1 organizes HP1 alpha for silencing of endogenous retroviral elements in embryonic stem cells.
Authors: Gaurav, N. / O'Hara, R. / Hyder, U. / Qin, W. / Her, C. / Romero, H. / Kumar, A. / Marcaida, M.J. / Singh, R.K. / Hovius, R. / Selvam, K. / Liu, J. / Martire, S. / Yao, Y. / Challa, A. / Dal ...Authors: Gaurav, N. / O'Hara, R. / Hyder, U. / Qin, W. / Her, C. / Romero, H. / Kumar, A. / Marcaida, M.J. / Singh, R.K. / Hovius, R. / Selvam, K. / Liu, J. / Martire, S. / Yao, Y. / Challa, A. / Dal Peraro, M. / Fierz, B. / Kono, H. / Cardoso, M.C. / Debelouchina, G.T. / Leonhardt, H. / D'Orso, I. / Banaszynski, L.A. / Kutateladze, T.G.
History
DepositionJun 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 5
B: Chromobox protein homolog 5
C: Chromobox protein homolog 5
D: Chromobox protein homolog 5
E: Transcription intermediary factor 1-beta peptide
F: Transcription intermediary factor 1-beta peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0469
Polymers30,5956
Non-polymers4513
Water99155
1
A: Chromobox protein homolog 5
C: Chromobox protein homolog 5
E: Transcription intermediary factor 1-beta peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4484
Polymers15,2983
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chromobox protein homolog 5
D: Chromobox protein homolog 5
F: Transcription intermediary factor 1-beta peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5985
Polymers15,2983
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.809, 107.809, 64.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Chromobox protein homolog 5 / Antigen p25 / Heterochromatin protein 1 homolog alpha / HP1 alpha


Mass: 7313.364 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX5, HP1A / Production host: Escherichia coli (E. coli) / References: UniProt: P45973
#2: Protein/peptide Transcription intermediary factor 1-beta peptide / TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-associated protein 1 / KAP-1 / KRAB-interacting ...TIF1-beta / E3 SUMO-protein ligase TRIM28 / KRAB-associated protein 1 / KAP-1 / KRAB-interacting protein 1 / KRIP-1 / Nuclear corepressor KAP-1 / RING finger protein 96 / RING-type E3 ubiquitin transferase TIF1-beta / Tripartite motif-containing protein 28


Mass: 670.821 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM28, KAP1, RNF96, TIF1B / Production host: Escherichia coli (E. coli)
References: UniProt: Q13263, RING-type E3 ubiquitin transferase
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.54 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→46.68 Å / Num. obs: 16886 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.028 / Rrim(I) all: 0.088 / Χ2: 1 / Net I/σ(I): 16.5 / Num. measured all: 159878
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.519 / Num. measured all: 11300 / Num. unique obs: 1763 / CC1/2: 0.937 / Rpim(I) all: 0.22 / Rrim(I) all: 0.564 / Χ2: 1.09 / Net I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→37.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.268 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 875 5.2 %RANDOM
Rwork0.2346 ---
obs0.2356 15941 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.319 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å2-1.1 Å2-0 Å2
2---2.19 Å20 Å2
3---7.12 Å2
Refinement stepCycle: 1 / Resolution: 2.4→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 30 55 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122199
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162136
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.8352956
X-RAY DIFFRACTIONr_angle_other_deg0.591.7854932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.387514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09210397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1464.7051066
X-RAY DIFFRACTIONr_mcbond_other5.1384.7041066
X-RAY DIFFRACTIONr_mcangle_it7.3828.3921322
X-RAY DIFFRACTIONr_mcangle_other7.388.3961323
X-RAY DIFFRACTIONr_scbond_it6.2845.321133
X-RAY DIFFRACTIONr_scbond_other6.2825.3241134
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.0799.5571635
X-RAY DIFFRACTIONr_long_range_B_refined11.00845.742264
X-RAY DIFFRACTIONr_long_range_B_other11.00245.792261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 56 -
Rwork0.321 1172 -
obs--100 %

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