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- PDB-9osc: Crystal structure of HP1gamma chromoshadow domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 9osc
TitleCrystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide
Components
  • Chromobox protein homolog 3
  • Transcription intermediary factor 1-beta
KeywordsTRANSCRIPTION / HP1 / CSD domain / KAP1
Function / homology
Function and homology information


senescence-associated heterochromatin focus / convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / chromatin lock complex / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / suppression of viral release by host / histone methyltransferase binding / chromo shadow domain binding / condensed chromosome, centromeric region ...senescence-associated heterochromatin focus / convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / chromatin lock complex / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / suppression of viral release by host / histone methyltransferase binding / chromo shadow domain binding / condensed chromosome, centromeric region / genomic imprinting / Generic Transcription Pathway / nuclear inner membrane / SUMO transferase activity / DNA methylation-dependent constitutive heterochromatin formation / : / Transcriptional Regulation by E2F6 / site of DNA damage / protein sumoylation / epithelial to mesenchymal transition / chromosome, centromeric region / cellular response to dexamethasone stimulus / pericentric heterochromatin / heterochromatin / embryo implantation / SUMOylation of transcription cofactors / positive regulation of DNA repair / transcription coregulator binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / euchromatin / RING-type E3 ubiquitin transferase / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / spindle / HCMV Early Events / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / transcription corepressor activity / nuclear envelope / rhythmic process / heterochromatin formation / chromatin organization / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / chromosome, telomeric region / protein kinase activity / chromatin remodeling / protein domain specific binding / innate immune response / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / 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
Chromobox protein homologue 3 / Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : ...Chromobox protein homologue 3 / 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 (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chromobox protein homolog 3 / Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSelvam, K. / Liu, J. / Singh, R.K. / Gaurav, N. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2026
Title: HP1 gamma self-assembles and cooperates with KAP1 in repression of long noncoding RNA AI662270 in ESCs.
Authors: Gaurav, N. / Qin, W. / Selvam, K. / Zhou, Z. / Liu, J. / Yin, Y. / Singh, R.K. / O'Hara, R.A. / Tavaf, Z. / Kumar, A. / Kono, H. / Narlikar, G.J. / Banaszynski, L.A. / Leonhardt, H. / Kutateladze, T.G.
History
DepositionMay 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: 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 3
C: Transcription intermediary factor 1-beta


Theoretical massNumber of molelcules
Total (without water)8,9372
Polymers8,9372
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.726, 60.726, 43.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-488-

VAL

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Components

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


Mass: 7580.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13185
#2: Protein/peptide Transcription intermediary factor 1-beta / 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: 1356.660 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.0 M LiCl2, 0.1 M citrate buffer pH 4.0, and 20% PEG6000

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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: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 9004 / % possible obs: 97 % / Redundancy: 11.7 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.012 / Rrim(I) all: 0.043 / Χ2: 1.378 / Net I/σ(I): 25.8 / Num. measured all: 105578
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.77-1.86.80.3623880.9390.9840.140.391.35685.7
1.8-1.838.70.3124100.9780.9940.1090.3321.37990.5
1.83-1.8711.20.2784210.9880.9970.0860.2911.42491.1
1.87-1.9111.70.2434290.9920.9980.0730.2541.45194.5
1.91-1.9511.80.1694420.9940.9980.0510.1771.53894.8
1.95-1.99120.1474220.9970.9990.0430.1531.46296.8
1.99-2.0412.20.1314350.9960.9990.0390.1371.52294.4
2.04-2.112.20.1054540.9970.9990.0310.111.55598.7
2.1-2.1612.70.0934370.9980.9990.0270.0971.68894.6
2.16-2.2312.60.0744600.99810.0210.0771.427100
2.23-2.3112.70.0654590.99910.0190.0671.47799.4
2.31-2.412.70.0564650.99910.0160.0591.3299.6
2.4-2.5112.60.0584510.99910.0170.061.369100
2.51-2.6412.60.0524700.99910.0150.0541.38399.8
2.64-2.8112.60.0484500.99910.0140.051.46199.8
2.81-3.0312.50.0424700.99910.0120.0441.40399.8
3.03-3.3312.20.0354720.99910.010.0371.246100
3.33-3.8111.90.034476110.010.0361.213100
3.81-4.811.50.0314880.99910.0090.0321.023100
4.8-5010.30.031505110.010.0320.86298.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→26.31 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.599 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23587 452 5.1 %RANDOM
Rwork0.20646 ---
obs0.20795 8474 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.77→26.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms552 0 0 33 585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012581
X-RAY DIFFRACTIONr_bond_other_d0.0010.016562
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.854788
X-RAY DIFFRACTIONr_angle_other_deg0.6181.7861301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.132574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.07955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17710106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02127
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_it2.4462.29284
X-RAY DIFFRACTIONr_mcbond_other2.4442.291284
X-RAY DIFFRACTIONr_mcangle_it3.6164.084353
X-RAY DIFFRACTIONr_mcangle_other3.6114.085354
X-RAY DIFFRACTIONr_scbond_it3.332.719297
X-RAY DIFFRACTIONr_scbond_other3.2272.719296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2354.825433
X-RAY DIFFRACTIONr_long_range_B_refined6.53225.97601
X-RAY DIFFRACTIONr_long_range_B_other6.43125.25597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 29 -
Rwork0.278 563 -
obs--87.7 %
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)
10.2659-0.00160.06791.5845-1.10180.8977-0.1014-0.07380.0187-0.10680.13940.01230.101-0.0685-0.03790.08950.0314-0.00430.0661-0.01450.037325.8386-11.299-12.1575
20.1708-0.660.733110.3783-4.17733.38740.0190.07250.02150.2483-0.1538-0.170.02450.27960.13480.01610.0145-0.00540.0418-0.01770.075938.353-0.1739-13.8939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 174
2X-RAY DIFFRACTION2C485 - 491

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